A quantum chemical investigation of the metal centres in cytochrome c oxidase

Quantum effects are often of key importance for the function of biological systems at molecular level. Cellular respiration, where energy is extracted from the reduction of molecular oxygen to water, is no exception. In this work, the end station of the electron transport chain in mitochondria, cytochrome c oxidase, is investigated using quantum chemical methodology. Cytochrome c oxidase contains two haems, haem a and haem a3. Haem a3, with its copper companion, CuB, is involved in the final reduction of oxygen into water. This binuclear centre receives the necessary electrons from haem a. Haem a, in turn, receives its electrons from a copper ion pair in the vicinity, called CuA. Density functional theory (DFT) has been used to clarify the charge and spin distributions of haem a, as well as changes in these during redox activity. Upon reduction, the added electron is shown to be evenly distributed over the entire haem structure, important for the accommodation of the prosthetic group within the protein. At the same time, the spin distribution of the open-shell oxidised state is more localised to the central iron. The exact spin density distribution has been disputed in the literature, however, different experiments indicating different distributions of the unpaired electron. The apparent contradiction is shown to be due to the false assumption of a unit amount of unpaired electron density; in fact, the oxidised state has about 1.3 unpaired electrons. The validity of the DFT results have been corroborated by wave function based coupled cluster calculations. Point charges, for use in classical force field based simulations, have been parameterised for the four metal centres, using a newly developed methodology. In the procedure, the subsystem for which point charges are to be obtained, is surrounded by an outer region, with the purpose of stabilising the inner region, both electronically and structurally. Finally, the possibility of vibrational promotion of the electron transfer step between haem a and a3 has been investigated. Calculating the full vibrational spectra, at DFT level, of a combined model of the two haems, revealed several normal modes that do shift electron density between the haems. The magnitude of the shift was found to be moderate, at most. The proposed mechanism could have an assisting role in the electron transfer, which still seems to be dominated by electron tunnelling.

Studies of solar and stellar flares using multi-instrument data

Solar flares were first observed by plain eye in white light by William Carrington in England in 1859. Since then these eruptions in the solar corona have intrigued scientists. It is known that flares influence the space weather experienced by the planets in a multitude of ways, for example by causing aurora borealis. Understanding flares is at the epicentre of human survival in space, as astronauts cannot survive the highly energetic particles associated with large flares in high doses without contracting serious radiation disease symptoms, unless they shield themselves effectively during space missions. Flares may be at the epicentre of man s survival in the past as well: it has been suggested that giant flares might have played a role in exterminating many of the large species on Earth, including dinosaurs. Having said that prebiotic synthesis studies have shown lightning to be a decisive requirement for amino acid synthesis on the primordial Earth. Increased lightning activity could be attributed to space weather, and flares. This thesis studies flares in two ways: in the spectral and the spatial domain. We have extracted solar spectra using three different instruments, namely GOES (Geostationary Operational Environmental Satellite), RHESSI (Reuven Ramaty High Energy Solar Spectroscopic Imager) and XSM (X-ray Solar Monitor) for the same flares. The GOES spectra are low resolution obtained with a gas proportional counter, the RHESSI spectra are higher resolution obtained with Germanium detectors and the XSM spectra are very high resolution observed with a silicon detector. It turns out that the detector technology and response influence the spectra we see substantially, and are important to understanding what conclusions to draw from the data. With imaging data, there was not such a luxury of choice available. We used RHESSI imaging data to observe the spatial size of solar flares. In the present work the focus was primarily on current solar flares. However, we did make use of our improved understanding of solar flares to observe young suns in NGC 2547. The same techniques used with solar monitors were applied with XMM-Newton, a stellar X-ray monitor, and coupled with ground based Halpha observations these techniques yielded estimates for flare parameters in young suns. The material in this thesis is therefore structured from technology to application, covering the full processing path from raw data and detector responses to concrete physical parameter results, such as the first measurement of the length of plasma flare loops in young suns.

How Can Sustainable Agricultural Systems Promote Food Security in a Changing Climate?

A theoretical framework of the link between climate change, rural development, sustainable agriculture, poverty, and food security is presented. Some options to respond to climate change are described. Current knowledge and potential effects on agricultural productivity is discussed. Necessary conditions for successful adaptation includes secured property rights to land, institutions that make market access possible and credit possibilities. The options of mitigation and enhanced adaptive capacity and the requirements for their implementation are discussed.

Impact of agricultural market liberalization on food security in developing countries : a comparative study of Kenya and Zambia

This research investigates the impacts of agricultural market liberalization on food security in developing countries and it evaluates the supply perspective of food security. This research theme is applied on the agricultural sector in Kenya and in Zambia by studying the role policies played in the maize sub-sector. An evaluation of selected policies introduced at the beginning of the 1980s is made, as well as an assessment of whether those policies influenced maize output. A theoretical model of agricultural production is then formulated to reflect cereal production in a developing country setting. This study begins with a review of the general framework and the aims of the structural adjustment programs and proceeds to their application in the maize sector in Kenya and Zambia. A literature review of the supply and demand synthesis of food security is presented with examples from various developing countries. Contrary to previous studies on food security, this study assesses two countries with divergent economic orientations. Agricultural sector response to economic and institutional policies in different settings is also evaluated. Finally, a dynamic time series econometric model is applied to assess the effects of policy on maize output. The empirical findings suggest a weak policy influence on maize output, but the precipitation and acreage variables stand out as core determinants of maize output. The policy dimension of acreage and how markets influence it is not discussed at length in this study. Due to weak land rights and tenure structures in these countries, the direct impact of policy change on land markets cannot be precisely measured. Recurring government intervention during the structural policy implementation period impeded efficient functioning of input and output markets, particularly in Zambia. Input and output prices of maize and fertilizer responded more strongly in Kenya than in Zambia, where the state often ceded to public pressure by revoking pertinent policy measures. These policy interpretations are based on the response of policy variables which are more responsive in Kenya than in Zambia. According the obtained regression results, agricultural markets in general, and the maize sub-sector in particular, responded more positively to implemented policies in Kenya, than in Zambia, which supported a more socialist economic system. It is observed in these results that in order for policies to be effective, sector and regional dimensions need to be considered. The regional and sector dimensions were not taken into account in the formulation and implementation of structural adjustment policies in the 1980s. It can be noted that countries with vibrant economic structures and institutions fared better than those which had a firm, socially founded system.