In this thesis methodological developments have been made for the description of flexible conjugated dyes in room temperature spectrum calculations. The methods in question target increased accuracy and efficiency by combining classical molecular dynamics (MD) simulations with time-dependent response theory spectrum calculations. For absorption and fluorescence spectroscopies a form of conformational averaging is used, where the final spectrum is obtained as an average of spectra calculated for geometries extracted from ground and excited state MD simulations. For infrared and Raman spectroscopies averaged spectra are calculated based on individual spectra, obtained for zero-temperature optimized molecular structures, weighted by conformational statistics from MD trajectories. Statistics for structural properties are also used in both cases to gain additional information about the systems, allowing more efficient utilization of computational resources. As it is essential that the molecular mechanics description of the system is highly accurate for methods of this nature to be effective, high quality force field parameters have been derived, describing the molecules of interest in either the MM3 or CHARMM force fields. These methods have been employed in the study of three systems. The first is a platinum(II) actylide chromophore used in optical power limiting materials, for which a ultraviolet/visible absorption spectrum has been calculated. The second is a family of molecular probes called luminescent conjugated oligothiophenes, used to detect and characterize amyloid proteins, for which both absorption and fluorescence spectra have been calculated. Finally, infrared and Raman spectra have been calculated for a group of branched oligothiophenes used in organic solar cells. In addition, solvation effects have been studied for conjugated poly\-eletrolytes in water, resulting in the development of two solvation models suitable for this class of molecules. The first uses a quantum meachanics/molecular mechanics (QM/MM) description, in which the solute mole\-cule is described using accurate quantum mechanical methods while the surrounding water molecules are described using point charges and polarizable point dipoles. The second discards the water entirely and removes the ionic groups of the solute. The QM/MM model provides highly accurate results while the cut-down model gives results of slightly lower quality but at a much reduced computational cost. Finally, a study of protein-dye interactions has been performed, with the goal of explaining changes in the luminescence properties of the LCO chromophores when in the presence of amyloid proteins. Results were less than conclusive.

The goal of the following thesis research was to develop a systematic approach for the refinement of low-resolution protein models, as a part of the protein structure prediction procedure. Significant progress has been made in the field of protein structure prediction and the contemporary methods are able to assemble correct topology for a large fraction of protein domains. But such approximate models are often not detailed enough for some important applications, including studies of reaction mechanisms, functional annotation, drug design or virtual ligand screening. The development of a method that could bring those structures closer to the native is then of great importance. The minimal requirements for a potential that can refine protein structures is the existence of a correlation between the energy with native similarity and the scoring of the native structure as being lowest in energy. Extensive tests of the contemporary all-atom physics-based force fields were conducted to assess their applicability for refinement. The tests revealed flatness of such potentials and enabled the identification of the key problems in the current approaches. Guided by these results, the optimization of the AMBER (ff03) force field was performed that aimed at creating a funnel shape of the potential, with the native structure at the global minimum. Such shape should facilitate the conformational search during refinement and drive it towards the native conformation. Adjusting the relative weights of particular energy components, and adding an explicit hydrogen bond potential significantly improved the average correlation coefficient of the energy with native similarity (from 0.25 for the original ff03 potential to 0.65 for the optimized force field). The fraction of proteins for which the native structure had lowest energy increased from 0.22 to 0.90. The new, optimized potential was subsequently used to refine protein models of various native-similarity. The test employed 47 proteins and 100 decoy structures per protein. When the lowest energy structure from each trajectory was compared with the starting decoy, we observed structural improvement for 70% of the models on average. Such an unprecedented result of a systematic refinement is extremely promising in the context of high-resolution structure prediction.

Os nitretos do grupo III (BN, AIN,Gan e InN) e suas ligas ternárias Al-GaN e InGaN proporcionam, recentemente, um extraordinário avanço na fabricação de dispositivos opto-eletrônicos operando na região do espectro correspondente ao verde-azul-UV e na produção de dispositivos eletrônicos de alta frequência, alta temperatura e alta potência. Estes materiais semicondutores de gap largo atraíram enorme atenção dos pesquisadores nos últimos anos. O objetivo desta tese é o estudo das propriedades vibracionais dos nitretos do grupo III referente tanto ao cristal perfeito, quanto ao cristal com defeito. Utilizamos como base a Teoria Clássica do Crital Harmônico e o Método das Funções de Green. Com a Teoria Clássica do Cristal Harmônico, juntamente com o Método do Valence Force Filed e o Método da Soma de Ewald, que permitem gerar a matriz dinâmica do sistema, determinamos o comportamento vibracional dos nitretos binários e das ligas ternárias. A utilização destes métodos permitiu a obtenção do espectro de fônons dos nitretos binários, e o estudo do comportamento dos modos ópticos em para as ligas ternárias. A partir da Função de Green do cristal perfeito e da Função de Green do cristal com defeito, obtivemos as frequências e os modos vibracionais localizados e ressonantes introduzidos pela impureza de C e As em GaN. A partir das densidades de estados do cristal perfeito e do cristal com defeito, calculamos a entropia de formação da vacância de N em GaN. Os resultados obtidos foram usados na interpretação de dados experimentais disponíveis na literatura, relativos às propriedades vibracionais dos nitretos na estrutura wurtzita, e na predição e análise de dados experimentais obtidos pelo grupo do Laboratório de Novos Materiais Semicondutores do Instituto de Física da USP para os nitretos zincblende. / The group-III nitrides (BN, AIN, GaN and InN) and their ternary alloys AlGaN and InGaN generated recently an extraordirlary progress in the production of optoelectronic devices operating in the green-blue-UV region of the spectrum, and in the production of electronic devices of high frequency, high temperature and high power. These wide gap semiconductor materials attracted enormous attention in the last years. The objective of this Thesis was to study the vibrational properties of the bulk III nitrides, without and with defects. To accomplish this study we used the Classic Theory of the Harmonic Crystal and the Method of the Green\'s Functions. With the Classic Theory of the Harmonic Crystal, together with the Valence Force Field Method and the Method of the Ewald\'s Sum, that allow to generate the dynamic matrix of the system, we determined the vibrational behavior of the binary nitrides and of the ternary alloys. The use of these methods allowed us to obtain the phonon spectra of the binary nitrides and to study the behavior of the optical modes at of the ternary alloys. Starting from the Green\'s Function of the perfect crystal and the Green\'s Function of the crystal with defect, we obtained the frequencies and the localized and resonant vibrational modes introduced by the C and As impurities in GaN. Starting from the densities of states of the perfect crystal and of the crystal with defect, we calculated the formation entropy of the N vacancy in GaN. The obtained results were used in the interpretation of experimental data related to the vibrational properties of the wurtzite nitrides available in the literature, and in the prediction and analysis of experimental results obtained for zincblende nitrides by the group of the New Semiconductors Materials Laboratory of t11c Physics Institute at USP.

Reducing the dimensionality of the original pattern space in a definition of feature space while maintaining discriminatory power for classification is a general goal in pattern recognition. To accomplish this goal in the area of ear biometrics a highly recognized work was proposed by D. Hurley in 2D space. We were inspired by his work and developed a new method for 3D data. In a different way to Hurley’s work we obtain a potential energy surface from 3D depth image which underlies the force field and associated vector field has its own characteristics. Our feature extraction is conducted by combining two different approaches; an algorithmic approach as well as an analytical approach, both are based on the vector force field and geometrical approach which is based on 3D ear surface. To validate the technique, the ICP algorithm is used. This work differs from Hurley’s work not only because of the algorithm, but also because of the nature of the 3D data which delivers topological information of the images. We exploit geometry to acquire surface information of the ear which yields richer features than the original work. The performance of the proposed method was evaluated using the University of Notre Dame (UND) collection J2 database and MATLAB has been used as the software package. / phone number: 0700099273

Multidisciplinary contemporary discourse involving science, philosophy and theology has explored themes of creation and human identity. Contemporary critiques of anthropocentricism stem from such discourse. The understanding of human beings as ‘spirited bodies’ rather than embodied spirits, arises from a non-reductionist physicalist standpoint. This is the point of departure for this thesis. The study attempts to explore the understanding of human beings as ‘spirited bodies’ from a non-reductionist physicalist view and as a metaphor for ‘fresh’ perspectives and insights that could potentially inform and/or shape a theologically grounded earth-keeping ethos on a different premise from the traditional dualistic hierarchical viewpoint. Methodologically, this study attempts to reflect a unitary approach to knowledge. The study views the subject through three prisms. Firstly it takes a retrospective look to account for perspectives that have shaped hierarchical views of creation based on a dualistic principle that in turn have shaped the human power-dominion relationship with the rest of creation that is deemed to have led to the devastating eco-crisis the world faces today. Secondly, it considers a non-reductionist physicalist viewpoint that has challenged dualistic anthropological views of being in favour of the conception of human beings as ‘spirited bodies’ and which places human beings in a continuum with the rest creation. Thirdly, it picks up on Moltmann’s Trinitarian and pneumatological views of creation which orient the theological framework anchored on the community and communion within the triune relationship. Human solidarity with the rest of creation is then posited as the nexus that converges the strands of these different perspectives. The juxtaposition of the Genesis 1 creation story with Zambian cosmogony constitutes ‘case studies’ that illustrate how the fresh perspectives on creation and human identity open up an ‘interpretive space’ that could locate human beings in a continuum with the rest of creation and offer insight for an alternative earth-keeping ethos. Human solidarity with the rest of creation thus critiques traditional western dualistic and hierarchical conceptions of creation on one hand, and serves as an orienting concept for the ‘fresh’ earth-keeping ethos this study proposes on the other. / Dissertation (MA Theol)--University of Pretoria, 2013. / gm2014 / Dogmatics and Christian Ethics / unrestricted

Due to the wide application of silica based systems ranging from microelectronics to nuclear waste disposal, detailed knowledge of water-silica interactions plays an important role in understanding fundamental processes, such as glass corrosion and the long term reliability of devices. In this dissertation, atomistic computer simulation methods have been used to explore and identify the mechanisms of water-silica reactions and the detailed processes that control the properties of the water-silica interfaces due to their ability to provide atomic level details of the structure and reaction pathways. The main challenges of the amorphous nature of the silica based systems and nano-porosity of the structures were overcome by a combination of simulation methodologies based on classical molecular dynamics (MD) simulations with Reactive Force Field (ReaxFF) and density functional theory (DFT) based ab initio MD simulations. Through the development of nanoporous amorphous silica structure models, the interactions between water and the complex unhydroxylated internal surfaces identified the unusual stability of strained siloxane bonds in high energy ring structure defects, as well as the hydroxylation reaction kinetics, which suggests the difficulty in using DFT methods to simulate Si-O bond breakage with reasonable efficiency. Another important problem addressed is the development of silica gel structures and their interfaces, which is considered to control the long term residual dissolution rate in borosilicate glasses. Through application of the ReaxFF classical MD potential, silica gel structures which mimic the development of interfacial layers during silica dissolution were created A structural model, consisting of dense silica, silica gel, and bulk water, and the related interfaces was generated, to represent the dissolution gel structure. High temperature evolution of the silica-gel-water (SGW) structure was performed through classical MD simulation of the system, and growth of the gel into the water region occurred, as well as the formation of intermediate range structural features of dense silica. Additionally, hydroxylated silica monomers (SiO4H4) and longer polymerized silica chains were formed in the water region, indicating that glass dissolution is occurring, even at short time frames. The creation of the SGW model provides a framework for a method of identifying how interfacial structures which develop at glass-water interfaces can be incorporated into atomistic models for additional analysis of the dissolution of silicates in water.

A straightforward means to include explicit hydrogen bonds within the Universal Force Field (UFF) is presented. Instead of treating hydrogen bonds as non-bonded interaction subjected to electrostatic and Lennard-Jones potentials, we introduce an explicit bond with a negligible bond order, thus maintaining the structural integrity of the H-bonded complexes and avoiding the necessity to assign arbitrary charges to the system. The explicit hydrogen bond changes the coordination number of the acceptor site and the approach is thus most suitable for systems with under-coordinated atoms, such as many metalorganic frameworks; however, it also shows an excellent performance for other systems involving a hydrogen-bonded framework. In particular, it is an excellent means for creating starting structures for molecular dynamics and for investigations employing more sophisticated methods. The approach is validated for the hydrogen bonded complexes in the S22 dataset and then employed for a set of metal-organic frameworks from the Computation-Ready Experimental database and several hydrogen bonded crystals including water ice and clathrates. We show that the direct inclusion of hydrogen bonds reduces the maximum error in predicted cell parameters from 66% to only 14%, and the mean unsigned error is similarly reduced from 14% to only 4%. We posit that with the inclusion of hydrogen bonding, the solvent-mediated breathing of frameworks such as MIL-53 is nowaccessible to rapid UFF calculations, which will further the aim of rapid computational scanning of metal-organic frameworks while providing better starting points for electronic structure calculations.

La maladie d’Alzheimer touche plus de 40 millions de personnes dans le monde et résulte de l’agrégation du peptide beta-amyloïde de 40/42 résidus. En dépit de nombreuses études expérimentales et théoriques, le mécanisme de formation des fibres et des plaques n’est pas élucidé, et les structures des espèces les plus toxiques restent à déterminer. Dans cette thèse, je me suis intéressée à deux aspects. (1) La détermination du noyau de nucléation (N*) de deux fragments (Aβ)16-22 et (Aβ)37-42. Mon approche consiste à déterminer les paramètres OPEP du dimère (Aβ)16-22 en comparant des simulations Monte Carlo sur réseau et des dynamiques moléculaires atomiques par échange de répliques. Les paramètres fonctionnant aussi sur le trimère (Aβ)16-22 et les dimères et trimères (Aβ)37-42, j’ai étudié la surface d’énergie libre des décamères et mes simulations montrent que N* est de 10 chaines pour (Aβ)16-22 et est supérieure à 20 chaines pour (Aβ)37-42. (2) J’ai ensuite étudié les structures du dimère (Aβ)1-40 par simulations de dynamique moléculaire atomistique par échanges de répliques. Cette étude, qui fournit les conformations d’équilibre du dimère Aβ1-40 en solution aqueuse, ouvre des perspectives pour une compréhension de l’impact des mutations pathogènes et protectrices au niveau moléculaire. / The neurodegenerative Alzheimer's disease (AD) is affecting more than 40 million people worldwide and is linked to the aggregation of the amyloid-β proteins of 40/42 amino acids. Despite many experimental and theoretical studies, the mechanism by which amyloid fibrils form and the 3D structures of the early toxic species in aqueous solution remain to be determined. In this thesis, I studied the structures of the eraly formed oligomers of the amyloid-β peptide and the critical nucleus size of two amyloid-β peptide fragments using either coarse-grained or all-atom simulations. First, at the coarse-grained level, I developed a lattice model for amyloid protein, which allows us to study the nucleus sizes of two experimentally well-characterized peptide fragments (Aβ)16-22 and (Aβ)37-42 of the Alzheimer's peptide (Aβ)1-42. After presenting a comprehensive OPEP force-field parameterization using an on-lattice protein model with Monte Carlo simulations and atomistic simulations, I determined the nucleus sizes of the two fragments. My results show that the nucleation number is 10 chains for (Aβ)16-22 and larger than 20 chains for (Aβ)37-42. This knowledge is important to help design more effective drugs against AD. Second, I investigated the structures of the dimer (Aβ)1-40 using extensive atomistic REMD simulations. This study provides insights into the equilibrium structure of the (Aβ)1-40 dimer in aqueous solution, opening a new avenue for a comprehensive understanding of the impact of pathogenic and protective mutations in early-stage Alzheimer’s disease on a molecular level.

A molecule can crystallise in more than one crystal structure, a common phenomenon in organic compounds known as polymorphism. Different polymorphic forms may have significantly different physical properties, and a reliable prediction would be beneficial to the pharmaceutical industry. However, crystal structure prediction (CSP) based on the knowledge of the chemical structure had long been considered impossible. Previous failures of some CSP attempts led to speculation that the thermodynamic calculations in CSP methodologies failed to predict the kinetically favoured structures. Similarly, regarding the stabilities of co-crystals relative to their pure components, the results from lattice energy calculations and full CSP studies were inconclusive. In this thesis, these problems are addressed using the state-of-the-art CSP methodology implemented in the GRACE software. Firstly, it is shown that the low-energy predicted structures of four organic molecules, which have previously been considered difficult for CSP, correspond to their experimental structures. The possible outcomes of crystallisation can be reliably predicted by sufficiently accurate thermodynamic calculations. Then, the polymorphism of 5- chloroaspirin is investigated theoretically. The order of polymorph stability is predicted correctly and the isostructural relationships between a number of predicted structures and the experimental structures of other aspirin derivatives are established. Regarding the stabilities of co-crystals, 99 out of 102 co-crystals and salts of nicotinamide, isonicotinamide and picolinamide reported in the Cambridge Structural Database (CSD) are found to be more stable than their corresponding co-formers. Finally, full CSP studies of two co-crystal systems are conducted to explain why the co-crystals are not easily obtained experimentally. / University of Bradford

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