Orientador: Pedro Luiz Onófrio Volpe / Tese (doutorado) - Universidade Estadual de Campinas, Instituto de Química / Made available in DSpace on 2018-08-16T00:48:59Z (GMT). No. of bitstreams: 1 Camargo_MarceloSilvanode_D.pdf: 5113129 bytes, checksum: 44e51a54bcc1176d6b50d7db1a17558d (MD5) Previous issue date: 2009 / Resumo: O objetivo deste trabalho é o estudo das propriedades locais de soluções líquidas binárias de não-eletrólitos. Para se alcançar tal objetivo, executou-se o cálculo dos valores das integrais de Kirkwood-Buff a partir de grandezas termodinâmicas, elaborado por Ben-Naim. Foram calculados valores para as integrais KB de uma solução de etanol em água a 298,15 K, dando-se especial ênfase a regiões de alta concentração de água. Outras grandezas locais, como o desvio da idealidade em relação a uma solução simétrica, também foram calculadas a partir dos resultados obtidos para as integrais KB. O enfoque diferencial de Koga foi utilizado de maneira a complementar a análise realizada com as integrais de Kirkwood-Buff, possibilitando um estudo mais aprofundado do sistema. Até onde o autor desta dissertação está familiarizado, a utilização conjunta destas duas ferramentas teóricas está sendo implementada pela primeira vez / Abstract: The objective of this work is the study of local properties of binary liquid solutions of non-electrolytes. To achieve this goal, Kirkwood-Buff integrals from thermodynamic quantities were obtained, as Ben-Naim has demonstrated. We obtained the values of Kirkwood-Buff integrals for a solution of ethanol in water at 298.15 K, with particular emphasis on areas of high concentration of water. Other local qantities, as the deviation of ideality with respect to a symmetric solution, were also calculated from the results obtained from KB integrals. Koga¿s Differential approach was used in order to complement the analysis provided by Kirkwood-Buff integrals, allowing further understanding of the system. As far as the author of this thesis is familiar, the joint use / Doutorado / Físico-Química / Mestre em Química

Master of Science / Department of Chemistry / Paul E. Smith / The increasing importance of ion-water interactions in the field of chemistry and biology is leading us to examine the structure and dynamic properties of molecules of interest, based on the application of computer-aided models using molecular dynamics simulations. To enable this type of MD study, a molecular mechanics force field was developed and implemented. Kirkwood-Buff theory has been proved to be a powerful tool to provide a link between molecular quantities and corresponding thermodynamic properties. Parameters are the vital basis of a force field. KB integrals and densities were used to guide the development of parameters which could describe the activity of aqueous solutions of interest accurately. In this work, a Kirkwood-Buff Force Field (KBFF) for MD simulation of ammonium sulfate, sodium sulfate, sodium perchlorate and sodium nitrate are presented. Comparison between the KBFF models and existing force fields for ammonium sulfate was also performed and proved that KBFF is very promising. Not only were the experimentally observed KB integrals and density reproduced by KBFF, but other properties like self diffusion constant and relative permittivity are also well produced.

Africans forcibly brought to the Americas during slavery came from very diverse cultural groups, languages, and geographical regions. African-derived creole cultures that were subsequently created in the Americas resulted from the interaction of various traditional African forms of knowledge and ideology, combined with elements from various Indigenous and European cultural groups and materials. Creating within the context of slavery, these complex set of experiences and choices made by Africans in the Americas resulted in an equally diverse range of fluid and complex relationships between various African-descended groups. In a similar vein, Africans in Jamaica developed and exhibited a multiplicity of cultural identities and a complex set of relationships amongst themselves, reflective of their varied cultural, political, social, and physical origins (Brathwaite 1971; Joyner 1984). In the context of late-eighteenth and early-nineteenth century Buff Bay, Jamaica, most Africans were enslaved by whites to serve as laborers on plantations. However, a smaller group of Africans emerged from enslavement on plantations to form their own autonomous Maroon communities, alongside the plantation context and within the system of slavery. These two groups, enslaved Africans and Maroons, had a very complex set of relationship and identities that were fluid and constantly negotiated within the Jamaican slave society that was in turn hostile to both groups. Using historical (archival), oral, and archaeological sources of data, this dissertation attempts to do two things: first, it examines the daily life conditions of enslaved Africans at a Jamaican coffee plantation, Orange Vale, in order to understand settlement patterns, house structures, access to goods, informal trade networks, and material culture in their village. With constraints on their freedom and general confinement to the plantation, how did enslavement affect the material world of the enslaved Africans at Orange Vale? What materials did they have access to, and how did they use them? Second, I examine their cultural, social, and political identities alongside their autonomously freed Maroon “kin,” the neighboring Charles Town Maroon community. Using a popular origin myth, I attempt to show how descendents of both groups explain the origin of their relationship, as well as use the myth to simultaneously create political bonds based on their blackness and differentiate themselves. I also examine how their various origin, experiences, and worldview were manifested late-eighteenth and early nineteenth century Buff Bay and its place in the revolutionary Atlantic world, on the eve of emancipation. / text

Studien undersöker 14 djurfiguriner från Arne Furumarks utgrävning av den sena bronsåldersbosättningen Sinda på Cypern. Figurinerna detaljstuderas med syftet att vidare förstå Sindas socio-kulturella miljö. De grupperas utifrån liknande drag, för att sedan analyseras utifrån de influenser som genomsyrade tiden. Figurinerna jämförs även med de från andra platser för att se om det existerade ett lokalt formspråk i Sinda. Genomgående betraktas figurinerna utifrån teorierna att föremåls betydelse påverkas av sin kontext, och att ting och människa är sammanbundna. Gravkontexten betraktas som figurinernas primära kontext, i motsats till Furumarks tidigare slutsatser. Sindas figuriner skiljer sig från de på andra platser, i huvudsak genom deras naturtrogna drag, även om det finns förenande aspekter. Sindas förmodade fokus på djurhållning visar sig i vilka djur som är representerade; tjurarnas betydelse låg i huvudsak vid fertilitetssymbolism, och även de andra djuren har en koppling till jordbruk och djurhållning. Det påtagliga mykenska inflytande påverkade utformandet av den typ som alla Sindas figuriner tillhör, de så kallade buff painted bulls. / This study examines 14 animal figurines found in the late bronze age settlement of Sinda during Arne Furumark’s excavation. The figurines are studied in detail with the purpose of better understanding the socio-cultural environment of Sinda. The figurines are grouped by similar traits and is analyzed based on the influences and ideas of the time. They are also compared to figurines from other places, to see if there existed a locality in style in Sinda. Throughout, the figurines are understood from the theories of the human-thing relationship and that the context affect the purpose of an object. The grave context is understood as the objects’ primary context, as opposed to Furumarks earlier conclusions. Sinda’s figurines differ from those of other places, mainly due to their naturalistic traits, although there are uniting attributes. Sinda’s presumed focus on livestock is apparent in the represented animals; the bulls signified fertility, and the other animals depicted also had a connection to agriculture and livestock. The apparent Mycenaean influence affected the shaping and development of the type of figurine found in Sinda, the so-called buff painted bulls.

Master of Science / Department of Biochemistry / Paul E. Smith / We are developing a force field (FF) for molecular dynamics (MD) simulations of peptides and small proteins that is grounded in the Kirkwood-Buff theory of solutions. Here we present the Kirkwood-Buff Force Field (KBFF) parameters for the aromatic amino acids, based upon simulations of binary mixtures of small molecules representative of these amino acids over their entire composition ranges (excluding Histidine). Many aromatics are not fully soluble in water, so they have instead been studied in solvents of methanol or toluene. The parameters were developed by studying the following binary solutions: Phenylalanine − benzene + methanol, toluene + methanol, and toluene + benzene; Tyrosine − toluene + phenol and toluene + p-Cresol; Tryptophan − pyrrole + methanol and indole + methanol; Histidine − pyrrole + methanol, pyridine + methanol, pyridine + water, histidine + water (at 0.25 molal), and histidine monohydrochloride + water (at 0.3 molal and 0.6 molal). Our simulations reproduce the Kirkwood-Buff integrals, which guarantees that the KBFF provides an adequate balance of solute-solvent, solute-solute, and solvent-solvent interactions. Additionally, we show that the KBFF does not sacrifice reproduction of other solution properties in order to achieve this improved description of intermolecular interactions. We present these results as validating evidence for the future use of the KBFF in simulations of peptides and small proteins.

Doctor of Philosophy / Department of Chemistry / Paul E. Smith / The impact of computer simulations has become quite significant especially with the development of supercomputers during the last couple of decades. They are used in a wide range of purposes such as exploring experimentally inaccessible phenomena and providing an alternative when experiments are expensive, dangerous, time consuming, difficult and controversial. In terms of applications in biological systems molecular modeling techniques can be used in rational drug design, predicting structures of proteins and circumstances where the atomic level descriptions provided by them are valuable for the understanding of the systems of interest. Hence, the potential of computer simulations of biomolecular systems is undeniable. Irrespective of the promising uses of computer simulations, it cannot be guaranteed that the results will be realistic. The precision of a molecular simulation depends on the degree of sampling achieved during the simulation while the accuracy of the results depends on the satisfactory description of intramolecular and intermolecular interactions in the system, i.e. the force field. Recently, we have been developing a force field for molecular dynamics simulations of biological systems based on the Kirkwood Buff (KB) theory of solutions, not only with an emphasis on the accurate description of intermolecular interactions, but also by reproducing several physical properties such as partial molar volume, compressibility and composition dependent chemical potential derivatives to match with respective experimental values. In this approach simulation results in terms of KB integrals can be directly compared with experimental data through a KB analysis of the solution properties and therefore it provides a simple and clear method to test the capability of the KB derived force field. Initially, we have provided a rigorous framework for the analysis of experimental and simulation data concerning open and closed multicomponent systems using the KB theory of solutions. The results are illustrated using computer simulations for various concentrations of the solutes Gly, Gly₂ and Gly₃ in both open and closed systems, and in the absence or presence of NaCl as a cosolvent. Then, we have attempted to quantify the interactions between amino acids in aqueous solutions using the KB theory of solutions. The results are illustrated using computer simulations for various concentrations of the twenty zwitterionic amino acids at ambient temperature and pressure. Next, several amino acids were also studied at higher temperatures and pressures and the results are discussed in terms of the preferential (solute over solvent) interactions between the amino acids. Finally, we have described our most recent efforts towards a complete force field for peptides and proteins. The results are illustrated using molecular dynamics simulations of several tripeptides, selected peptides and selected globular proteins at ambient temperature and pressure followed by replica exchange molecular dynamics simulations of a few selected peptides.

Master of Science / Division of Biology / Samantha M. Wisely / Range-wide estimates of shorebird (Aves: Charadriiformes) populations suggest sharp declines in population sizes across a range of species. Efforts to accurately assess the conservation status of wild populations are becoming increasingly vital to species management. One shorebird of conservation concern, the Buff-breasted Sandpiper (Tryngites subruficollis), is a New World migrant which winters in southeastern South America and breeds in the arctic. To establish an updated conservation status for Buff-breasted Sandpipers, we conducted a molecular survey of wild populations on spatial and temporal scales. We analyzed patterns of global population structure, demographic trends, and phylogeography using nine polymorphic microsatellites and two mitochondrial DNA (mtDNA) markers, cytochrome b and the control region, among 477 individuals across their distributional range. To empirically assess the impact of population declines on genetic diversity, we also surveyed segments of the same two mtDNA markers from 220 museum specimens collected across a 135-year period. Contemporary microsatellite and mtDNA analyses revealed that Buff-breasted Sandpipers are admixed on a global scale, with effective population size estimates ranging from 2,657 to 16,400 birds and no signal of a recent genetic bottleneck. Contemporary mtDNA analyses suggested a pattern of haplotype diversity consistent with a historic radiation from a single refugium which we estimated to have occurred between 8,000−45,000 years before present. Using five measures of mtDNA diversity (haplotype and nucleotide diversity, trend analyses of haplotype richness, Watterson’s estimate of theta, and phi-statistics), as well as a Bayesian Skyline reconstruction of demographic trends in effective population size (N[subscript]e[subscript]f), we concluded that substantial mtDNA diversity and N[subscript]e[subscript]f had not been lost as a result of the population declines in this species. While genetic diversity did not appear to have been lost due to population losses, management efforts must focus on preventing future losses in order for wild populations to remain viable. Our results suggested that the global population of Buff-breasted Sandpipers should be treated as a single, panmictic conservation unit and that successful management must focus on preventing further declines and habitat fragmentation.

Doctor of Philosophy / Department of Chemistry / Paul E. Smith / Kirkwood Buff (KB) theory is one of the most important theories of solutions. The theory can relate integrals over radial (pair) distribution functions (rdfs) in the grand canonical ensemble to common thermodynamic properties. An inversion of the KB theory has been proposed by Ben-Naim and this has led to the wide spread popularity of KB theory. The idea of the KB inversion procedure is to calculate KB integrals from available thermodynamic properties. The KB theory can be used to validate the force field (ff) parameters used in molecular dynamics simulations. We have tested a series of small molecule ff parameters using KB theory that consists of both atom centered partial atomic charges and extra charge sites. The results indicate that using extra charge sites, derived from QM calculations, does not necessarily provide a more accurate representation of condensed phase properties. A further study aimed at an ongoing project of deriving new biomolecular ff parameters based on KB theory, has developed ff parameters for esters in order to represent the ester conjugation of the phospholipid molecule. The models were further tested against experimental properties. Preferential solvation (PS) is an important concept of solution mixtures that can be described using KB theory. The difference between local composition and bulk composition in solution mixtures leads to the concept of PS. A generalized explanation based on local mole fractions was derived by Ben-Naim using KB theory. However, the original expressions have been modified over years. Here, we propose a new approach based on local volume fractions to explore PS in binary and ternary solution mixtures. Experimental and simulation data were used to examine different approaches to PS. A relationship between the rdf and the triplet distribution function can be obtained using the Kirkwood Superposition Approximation (KSA). A combination of Fluctuation Solution Theory and experimental rdfs are used to examine the KSA at a series of state points for pure water. The accuracy of several other approximate relationships between the pair and triplet correlation functions was also investigated and are in good agreement for regions of the phase diagram where the compressibility is small.

Cette thèse se concentre sur l’iconographie des céramiques polychromes à pâte argileuse jaunâtre, connues sous le nom de buff ware et attribuées à Nishapur aux IXe-Xe siècles. Ces céramiques ont la particularité d’être décorées par des scènes à figures humaines, animales et d‘oiseaux souvent sur un fond jaune vif, peintes de couleurs vertes et noires et parfois rouges. Depuis leur découverte en 1935, l’iconographie de ces scènes est restée un sujet de débat parmi les chercheurs, sans réponse définitive. Cette recherche vise à apporter un regard complémentaire sur cette production originale de céramiques d’Iran oriental. Le but de cette étude est de revisiter les questions et les réponses existantes, et aussi d’aborder de nouvelles hypothèses. Les questions comprennent la connaissance, la production et l’iconographie de ces céramiques. La première partie de cette étude expose l’histoire et les différents aspects géographiques et socioculturels de la ville médiévale de Nishapur. Dans la deuxième partie sont étudiées la production, la distribution, la chronologie et la morphologie de ces céramiques afin de définir leurs caractéristiques. La troisième partie est consacrée à l’identification des scènes représentées sur les céramiques polychromes de Nishapur et à l’analyse de leur iconographie. Y sont proposées plusieurs hypothèses sur l’iconographie des scènes liée à la mythologie persane, aux traditions, aux légendes, aux croyances et aux rituels. Cette recherche est basée sur une étude approfondie de 30 céramiques principales, 139 céramiques complémentaires et 35 objets de comparaison, représentés dans un catalogue de trois corpus. / This dissertation focuses on the iconography of polychrome ceramics having a buff body, known as buff wares and attributed to Nishapur in the 9th-10th centuries. These ceramics were decorated with scenes of human, animal and bird figures, often on a bright yellow background and painted in green, black and sometimes red. Since their discovery in 1935, the iconography of these scenes has remained a subject of research with no definitive result. The research aims to provide a complementary fresh look at this original ceramic production of eastern Iran. The intention of this study is to revise the existing questions and answers, and to approach new hypothesis. The questions concern the characterization, the production and the iconography of these ceramics. The first part of this study exposes history and different geographical and sociocultural aspects of the medieval city of Nishapur. The second part of the study inquires the production, the distribution, the chronology and the morphology of theses ceramics. The third part focuses on the iconography of the scenes represented on Nishapur buff wares. It proposes a number of hypothesis on the iconography of the scenes related to Persian mythology, traditions, legends, beliefs and rituals. This research is based on a detailed study on 30 main wares, 139 complementary ceramics and 35 comparison objects, represented in a catalogue, which is completed by detailed drawings of the ceramics.

Doctor of Philosophy / Department of Chemistry / Paul E. Smith / In the study of biological systems, molecular dynamics (MD) simulations have played an important role in providing atomic details for phenomena of interest. The force field used in MD simulations is a critical factor determining the quality of the simulations. Recently, Kirkwood-Buff (KB) theory has been applied to study preferential interactions and to develop a new force field. KB theory provides a path from quantities determined from simulation data to the corresponding thermodynamic data. Here we combine KB theory and molecular simulations to study a variety of intermolecular interactions in solution. First, recent results concerning the formulation and evaluation of preferential interactions in biological systems in terms of KB integrals are presented. In particular, experimental and simulated preferential interactions of a cosolvent with a biomolecule in the presence of water are described. Second, a force field for the computer simulation of aqueous solutions of amides is presented. The force field is designed to reproduce the experimentally observed density and KB integrals for N-methylacetamide (NMA), allowing for an accurate description of the NMA activity. Other properties such as the translational diffusion constant and heat of mixing are also well reproduced. The force field is then extended to include N,N'-dimethylacetamide and acetamide with good success. The models presented here provide a basis for an accurate force field for peptides and proteins. Comparison between the developed KB force fields (KBFF) and existing force fields is performed for amide and glycine and proves that the KBFF approach is competitive. Also, explicit expressions are developed for the chemical potential derivatives, partial molar volumes, and isothermal compressibility of solution mixtures involving four components at finite concentrations using the KB theory of solutions. A general recursion relationship is also provided which can be used to generate the chemical potential derivatives for higher component solutions. Finally, a pairwise preferential interaction model (PPIM), described by KB integrals is developed to quantify and characterize the interactions between functional groups observed in peptides.