No description available.

A low-cost fibre-optic probe was constructed, and used to provide an optical link between an FT-Raman spectrometer and a Differential Scanning Calorimeter (DSC). The resulting Simultaneous Raman-DSC (SRD) method combines the vibrational structural information of FT-Raman spectroscopy with the thermal data of DSC, which is particularly useful for characterisation of samples exhibiting temperature- and thermal conditioning-dependent polymorphic (i. e. structural) changes. The samples chosen for method development and structural study were ammonium nitrate (NH4NO3), the triglyceride sn-1,3-distearoyl-2-oleoyl glycerol (SOS), cocoa butter (which is chiefly composed of a mixture of monounsaturated triglycerides), and some chocolates of differing composition. The bifurcated `6-around-i' parallel fibres probe design allowed Raman spectra to be collected from unencapsulateds amplesi n the normal DSC sample position without extensive mechanical modifications or the use of extra optical components. Method development using the above samples showed that the combined SRD sampling has various effects on collected data. With this probe design, a "glass background" spectrum is superimposed on the Raman spectrum, and must be subtracted using the spectrometer software. At raised temperatures, a thermal emission feature appears in the Raman spectrum at high wavenumber shift. The incident laser light was found to raise sample temperatures by around 1.5-3K. Raman spectra were therefore collected with samples held around 10K below transition onset temperatures. The necessary lack of encapsulation resulted in broadened thermal transitions in DSC heating curves, and potential heat loss due to radiative emission at raised temperatures. However, for samples analysed near room temperature, onset melting points for transitions with the laser off were not significantly altered by SRD sampling. Ammonium nitrate is often irreproducible in it's exact phase transition thermal behaviour. SRD analysis showed the expected phases IV, III, II and I at room temperature and above at normal atmospheric pressure. Raman spectra could then be unambiguously assigned to the respective phases. Comparison with previous literature work allows the spectral changes seen to be interpreted using symmetry-based rationalisations. The triglyceride SOS was found to conform well to the literature thermal behaviour. SRD analysis showed DSC heating curves with onset melting points and features identifying the polymorphs produced as a, , y, ß', ß2 and [il. A literature survey allows the corresponding Raman spectra to be interpreted in the light of structural packing suggestions made by workers using various other analytical techniques. Cocoa butter was successfully prepared in states 3,4,5 and 6 of the six polymorphs known to exist. DSC melting behaviour and heating curve shapes were used to unambiguously relate Raman spectra to the individual polymorphs. Interpretation of Raman spectra was based on the SOS triglyceride SRD results, together with structural packing suggestions from the literature. A selection of chocolate samples were also analysed by SRD. Those with a high cocoa butter content were found to approximate well to the thermal and structural behaviour of pure cocoa butter.

This research investigates through computational methods whether the physical properties of DNA contribute to its harmonic signature, the uniqueness of that signature if present, and motion of the DNA molecule in water. When DNA is solvated in water at normal 'room temperature', it experiences a natural vibration due to the Brownian motion of the particles in the water colliding with the DNA. The null hypothesis is that there is no evidence to suggest a relationship between DNA's motion and strand length, while the alternative hypothesis is that there is evidence to suggest a relationship between DNA's vibrational motion and strand length. In a similar vein to the first hypothesis, a second hypothesis posits that DNA's vibrational motion may be dependent on strand content. The nature of this relationship, whether linear, exponential, logarithmic or non-continuous is not hypothesized by this research but will be discovered by testing if there is evidence to suggest a relationship between DNA's motion and strand length. The research also aims to discover whether the motion of DNA, when it varies by strand length and/or content, is sufficiently unique to allow that DNA to be identified in the absence of foreknowledge of the type of DNA that is present in a manner similar to a signature. If there is evidence to suggest that there is a uniqueness in DNA's vibrational motion under varying DNA strand content or length, then additional experimentation will be needed to determine whether these variances are unique across small changes as well as large changes, or large changes only. Finally, the question of whether it might be possible to identify a strand of unique DNA by base pair configuration solely from its vibrational signature, or if not, whether it might be possible to identify changes existing inside of a known DNA strand (such as a corruption, transposition or mutational error) is explored. Given the computational approach to this research, the NAMD simulation package (released by the Theoretical and Computational Biophysics Group at the University of Illinois at Urbana-Champaign) with the CHARMM force field would be the most appropriate set of tools for this investigation (Phillips et al., 2005), and will therefore be the toolset used in this research. For visualization and manipulation of model data, the VMD (Visual Molecular Dynamics) package will be employed. Further, these tools may be optimized and/or be aware of nucleic acid structures, and are free. These tools appear to be sufficient for this task, with validated fidelity of the simulation to provide vibrational and pressure profile data that could be analyzed; sufficient capabilities to do what is being asked of it; speed, so that runs can be done in a reasonable period of time (weeks versus months); and parallelizability, so that the tool could be run over a clustered network of computers dedicated to the task to increase the speed and capacity of the simulations. The computer cluster enabled analysis of 30,000 to 40,000 atom systems spending more than 410,000 CPU computational hours of hundreds of nano second duration, experimental runs each sampled 500,000 times with two-femtosecond “frames.” Using Fourier transforms of run pressure readings into frequencies, the simulation investigation could not reject the null hypotheses that the frequencies observed in the system runs are independent on the DNA strand length or content being studied. To be clear, frequency variations were present in the in silicon replications of the DNA in ionized solutions, but we were unable to conclude that those variations were not due to other system factors. There were several tests employed to determine alternative factors that caused these variations. Chief among the factors is the possibility that the water box itself is the source of a large amount of vibrational noise that makes it difficult or impossible with the tools that we had at our disposal to isolate any signals emitted by the DNA strands. Assuming the water-box itself was a source of large amounts of vibrational noise, an emergent hypothesis was generated and additional post-hoc testing was undertaken to attempt to isolate and then filter the water box noise from the rest of the system frequencies. With conclusive results we found that the water box is responsible for the majority of the signals being recorded, resulting in very low signal amplitudes from the DNA molecules themselves. Using these low signal amplitudes being emitted by the DNA, we could not be conclusively uniquely associate either DNA length or content with the remaining observed frequencies. A brief look at a future possible isolation technique, wavelet analysis, was conducted. Finally, because these results are dependent on the tools at our disposal and hence by no means conclusive, suggestions for future research to expand on and further test these hypothesis are made in the final chapter.

No description available.

Orientador: Roberto Naves Domingos / Banca: Alberto Ibãnez Ruiz / Banca: Dermeval José Mazzini Sartori / Resumo: A cultura de cana-de-açúcar no Brasil ocupa uma extensa área, devido a sua importância econômica e seu potencial na obtenção de bioenergia. É importante saber como esta cultura irá responder ao aumento previsto na concentração de gás carbônico (CO2) atmosférico, uma vez que é um composto chave nos processos das mudanças climática globais. Sabendo que esse gás é emitido tanto pelas folhas como pelas raízes das plantas e difundido pelo solo, o objetivo desse trabalho foi desenvolver uma metodologia para a quantificação de CO2 de solo em condições de laboratório para simular as situações de campo em ambiente controlado. A abordagem utilizou 15 frascos de vidro com capacidade para 2,8 L, fechados com sistema de válvulas para entrada de ar e saída de CO2 acoplados a um analisador de gases LI-COR 840. O experimento também envolveu coleta de solos em área de Latossolo Vermelho Distroférrico típico de textura argilosa, com cultura de cana-deaçúcar em três localidades, sendo uma área coberta com palhada e plantas adultas, outra área arada e gradeada com colmo em brota e outra área desnuda em descanso após colheita de soja. Estas amostras foram peneiradas com malhas de 2,5 mm e 5 mm e secas na sombra ao ar livre num período de 25 dias. Em cada frasco foi acondicionado 1300 g de solo por 20 dias para verificar a atividade do solo em formação de CO2, que foi medida pela câmara respirométrica a qual possui leitor ótico de raios infravermelho não dispersivo, capaz de medir CO2 ativo por vibrações moleculares. Os dados obtidos no sistema demonstraram formação de um valor médio de 483,85 ppm de emissão de CO2, valor este que condiz com o meio natural quando isento de vegetação / Abstract: The cultivation of sugar cane in Brazil occupies a large area due to the economic importance of this crop and its potential for bioenergy. It is important to know how the crop will respond to the increase in the concentration of carbon dioxide (CO2) in the atmosphere, since this gas is a key component in the processes of global climate change. This gas is emitted by both the leaves and the roots of plants and distributed throughout the soil. The objective of this study was to develop a methodology for the measurement of CO2 from soil in laboratory conditions to simulate field situations in a controlled environment. The approach used 15 glass bottles with a capacity of 2.8 L, closed with a valve system for air intake and CO2 output coupled to a gas analyzer LI-COR 840. The study also involved collection of soil in the area of Hapludox clayey, with growing sugar cane in three locations and an area covered with straw and adult plants, another area plowed and fenced with sprouts and in stem other denuded areas at rest after soybean harvest. These samples were sieved with meshes of 2.5 mm and 5 mm and dried in the shade outdoors in a period of 25 days. In each vial, samples were taken each day for 20 days consisting of 1300 g of soil to verify the activity of soil formation of CO2, which was measured by the respiration chamber, which has an optical reader of non-dispersive infrared rays, capable of measuring CO2 by active molecular vibrations. The data obtained in the system showed the formation of an average of 483.85 ppm of CO2 emissions, a figure that matches the natural environment when free of vegetation / Mestre

Made available in DSpace on 2014-06-11T19:25:32Z (GMT). No. of bitstreams: 0 Previous issue date: 2010-05-31Bitstream added on 2014-06-13T19:32:42Z : No. of bitstreams: 1 leite_vdpo_me_rcla.pdf: 4581751 bytes, checksum: 69f0eaf0a28577e952aa235b12b6f1e6 (MD5) / Universidade Estadual Paulista (UNESP) / A cultura de cana-de-açúcar no Brasil ocupa uma extensa área, devido a sua importância econômica e seu potencial na obtenção de bioenergia. É importante saber como esta cultura irá responder ao aumento previsto na concentração de gás carbônico (CO2) atmosférico, uma vez que é um composto chave nos processos das mudanças climática globais. Sabendo que esse gás é emitido tanto pelas folhas como pelas raízes das plantas e difundido pelo solo, o objetivo desse trabalho foi desenvolver uma metodologia para a quantificação de CO2 de solo em condições de laboratório para simular as situações de campo em ambiente controlado. A abordagem utilizou 15 frascos de vidro com capacidade para 2,8 L, fechados com sistema de válvulas para entrada de ar e saída de CO2 acoplados a um analisador de gases LI-COR 840. O experimento também envolveu coleta de solos em área de Latossolo Vermelho Distroférrico típico de textura argilosa, com cultura de cana-deaçúcar em três localidades, sendo uma área coberta com palhada e plantas adultas, outra área arada e gradeada com colmo em brota e outra área desnuda em descanso após colheita de soja. Estas amostras foram peneiradas com malhas de 2,5 mm e 5 mm e secas na sombra ao ar livre num período de 25 dias. Em cada frasco foi acondicionado 1300 g de solo por 20 dias para verificar a atividade do solo em formação de CO2, que foi medida pela câmara respirométrica a qual possui leitor ótico de raios infravermelho não dispersivo, capaz de medir CO2 ativo por vibrações moleculares. Os dados obtidos no sistema demonstraram formação de um valor médio de 483,85 ppm de emissão de CO2, valor este que condiz com o meio natural quando isento de vegetação / The cultivation of sugar cane in Brazil occupies a large area due to the economic importance of this crop and its potential for bioenergy. It is important to know how the crop will respond to the increase in the concentration of carbon dioxide (CO2) in the atmosphere, since this gas is a key component in the processes of global climate change. This gas is emitted by both the leaves and the roots of plants and distributed throughout the soil. The objective of this study was to develop a methodology for the measurement of CO2 from soil in laboratory conditions to simulate field situations in a controlled environment. The approach used 15 glass bottles with a capacity of 2.8 L, closed with a valve system for air intake and CO2 output coupled to a gas analyzer LI-COR 840. The study also involved collection of soil in the area of Hapludox clayey, with growing sugar cane in three locations and an area covered with straw and adult plants, another area plowed and fenced with sprouts and in stem other denuded areas at rest after soybean harvest. These samples were sieved with meshes of 2.5 mm and 5 mm and dried in the shade outdoors in a period of 25 days. In each vial, samples were taken each day for 20 days consisting of 1300 g of soil to verify the activity of soil formation of CO2, which was measured by the respiration chamber, which has an optical reader of non-dispersive infrared rays, capable of measuring CO2 by active molecular vibrations. The data obtained in the system showed the formation of an average of 483.85 ppm of CO2 emissions, a figure that matches the natural environment when free of vegetation

科学研究費補助金 研究種目:一般研究(C) 課題番号:01540396 研究代表者:高塚 和夫 研究期間:1989-1990年度

Ce travail présente une étude théorique des spectres RMN de molécules biologiques. Dans la première partie, les calculs DFT des paramètres RMN (déplacements chimiques et constantes de couplage spin-spin) pour les protons liés à des atomes de carbone ont été réalisés pour quatre métabolites de la prostate: la putrescine, la spermidine, la spermine, et la sarcosine, et trois métabolites du cerveau: l'acétate, l'alanine et la sérine. Une étude théorique systématique, dans l'approche DFT, des paramètres de RMN des métabolites a montré que la méthode B3LYP/6-311++G** est un bon compromis entre la précision et les coûts. Les contributions du solvant ont été évaluées en utilisant le modèle PCM, les effets des isomères, pondérés dans l’approximation de Boltzmann, ont été pris en compte, et les corrections de vibration de point zéro ont été estimées en utilisant une approche perturbative au second ordre. La comparaison avec l'expérience a démontré que tous ces effets sont nécessaires pour améliorer l'accord entre les données calculées et expérimentales, aboutissant à des résultats de grande précision. Dans la deuxième partie, nous avons développé un nouveau modèle, BioShift, qui permet la prédiction des déplacements chimiques des différents noyaux (H, N, C ...) pour des molécules biologiques (protéines, ADN, ARN, polyamine ...). Il est simple, rapide, et comporte un nombre limité de paramètres. La comparaison avec des modèles sophistiqués conçus spécialement pour la prédiction des déplacements chimiques des protéines a montré que Bioshift est concurrentiel avec de tels modèles. / The present work presents a theoretical study of the NMR spectra of biological molecules. In the first part, DFT calculations of the spin-Hamiltonian NMR parameters (chemical shifts and spin-spin coupling constants) for protons attached to carbon atoms have been performed for four prostate metabolites: putrescine, spermidine, spermine, and sarcosine, and three brain metabolites: acetate, alanine, and serine. A theoretical investigation, within the DFT approach, of the NMR parameters of metabolites has shown that the B3LYP/6-311++G** level of calculation is a good compromise between accuracy and costs. Contributions from solvent were evaluated using the PCM model, Boltzmann weighted isomer effects were calculated, and zero-point vibrational corrections were estimated using a second order perturbation approach. Comparison with experiment has demonstrated that all these effects are necessary to improve the agreement between calculated and experimental data. In the second part, we have presented a new model, BioShift, that allows the prediction of chemical shifts of different nuclei (H, N, C…) for biological molecules (proteins, DNA, RNA, polyamine …). It is simple, fast, and involves a limited number of parameters. Comparison with well-known sophisticated models designed especially for the prediction of chemical shifts of proteins showed that Bioshift is competitive with such models.