Theoretical Studies on Coupled Electron and Proton Transfer in Cytochrome c Oxidase

The complexity of life is based on an effective energy transduction machinery, which has evolved during the last 3.5 billion years. In aerobic life, the utilization of the high oxidizing potential of molecular oxygen powers this machinery. Oxygen is safely reduced by a membrane bound enzyme, cytochrome c oxidase (CcO), to produce an electrochemical proton gradient over the mitochondrial or bacterial membrane. This gradient is used for energy-requiring reactions such as synthesis of ATP by F0F1-ATPase and active transport. In this thesis, the molecular mechanism by which CcO couples the oxygen reduction chemistry to proton-pumping has been studied by theoretical computer simulations. By building both classical and quantum mechanical model systems based on the X-ray structure of CcO from Bos taurus, the dynamics and energetics of the system were studied in different intermediate states of the enzyme. As a result of this work, a mechanism was suggested by which CcO can prevent protons from leaking backwards in proton-pumping. The use and activation of two proton conducting channels were also enlightened together with a mechanism by which CcO sorts the chemical protons from pumped protons. The latter problem is referred to as the gating mechanism of CcO, and has remained a challenge in the bioenergetics field for more than three decades. Furthermore, a new method for deriving charge parameters for classical simulations of complex metalloenzymes was developed.

Experimental studies of lipped channel beams subject to web crippling under two-flange load cases

Lipped channel beams (LCBs) are commonly used as flexural members such as floor joists and bearers in the construction 6 industry. These thin-walled LCBs are subjected to specific buckling and failure modes, one of them being web crippling. Despite considerable 7 research in this area, some recent studies have shown that the current web crippling design rules are unable to predict the test capacities under 8 end-two-flange (ETF) and interior-two-flange (ITF) load conditions. In many instances, web crippling predictions by the available design 9 standards such as AISI S100, AS/NZS 4600 and Eurocode 3 Part 1-3 are inconsistent, i.e., unconservative in some cases, although they 10 are conservative in other cases. Hence, experimental studies consisting of 36 tests were conducted in this research to assess the web crippling 11 behavior and capacities of high-strength LCBs under two-flange load cases (ETF and ITF). Experimental results were then compared with the 12 predictions from current design rules. Comparison of the ultimate web crippling capacities from tests showed that the design equations are 13 very unconservative for LCB sections under the ETF load case and are conservative for the ITF load case. Hence, improved equations were 14 proposed to determine the web crippling capacities of LCBs based on the experimental results from this study. Current design equations do 15 not provide the direct strength method (DSM) provisions for web crippling. Hence, suitable design rules were also developed under the DSM 16 format using the test results and buckling analyses using finite-element analyses.

The visual preferences for forest regeneration and field afforestation - four case studies in Finland

The overall aim of this dissertation was to study the public's preferences for forest regeneration fellings and field afforestations, as well as to find out the relations of these preferences to landscape management instructions, to ecological healthiness, and to the contemporary theories for predicting landscape preferences. This dissertation includes four case studies in Finland, each based on the visualization of management options and surveys. Guidelines for improving the visual quality of forest regeneration and field afforestation are given based on the case studies. The results show that forest regeneration can be connected to positive images and memories when the regeneration area is small and some time has passed since the felling. Preferences may not depend only on the management alternative itself but also on the viewing distance, viewing point, and the scene in which the management options are implemented. The current Finnish forest landscape management guidelines as well as the ecological healthiness of the studied options are to a large extent compatible with the public's preferences. However, there are some discrepancies. For example, the landscape management instructions as well as ecological hypotheses suggest that the retention trees need to be left in groups, whereas people usually prefer individually located retention trees to those trees in groups. Information and psycho-evolutionary theories provide some possible explanations for people's preferences for forest regeneration and field afforestation, but the results cannot be consistently explained by these theories. The preferences of the different stakeholder groups were very similar. However, the preference ratings of the groups that make their living from forest - forest owners and forest professionals - slightly differed from those of the others. These results provide support for the assumptions that preferences are largely consistent at least within one nation, but that knowledge and a reference group may also influence preferences.

Experimental studies on web crippling strength of hollow flange channels under EOF and IOF load cases

LiteSteel beam (LSB) is a hollow flange channel made from cold-formed steel using a patented manufacturing process involving simultaneous cold-forming and dual electric resistance welding. LSBs are currently used as floor joists and bearers in buildings. However, there are no appropriate design standards available due to its unique hollow flange geometry, residual stress characteristics and initial geometric imperfections arising from manufacturing processes. Recent research studies have focused on investigating the structural behaviour of LSBs under pure bending, predominant shear and combined actions. However, web crippling behaviour and strengths of LSBs still need to be examined. Therefore, an experimental study was undertaken to investigate the web crippling behaviour and strengths of LSBs under EOF (End One Flange) and IOF (Interior One Flange) load cases. A total of 23 web crippling tests were performed and the results were compared with the current AS/NZS 4600 and AISI S100 design standards, which showed that the cold-formed steel design rules predicted the web crippling capacity of LSB sections very conservatively under EOF and IOF load cases. Therefore, suitably improved design equations were proposed to determine the web crippling capacity of LSBs based on experimental results. In addition, new design equations were also developed under the Direct Strength Method format. This paper presents the details of this experimental study on the web crippling behaviour and strengths of LiteSteel beams under EOF and IOF load cases and the results.

Experimental and numerical studies of hollow flange channel beams subject to web crippling under ETF and ITF load cases

This paper presents the details of experimental and numerical studies on the web crippling behaviour of hollow flange channel beams, known as LiteSteel beams (LSB). The LSB has a unique shape of a channel beam with two rectangular hollow flanges, made using a unique manufacturing process. Experimental and numerical studies have been carried out to evaluate the behaviour and design of LSBs subject to pure bending actions, predominant shear actions and combined actions. To date, however, no investigation has been conducted into the web crippling behaviour and strength of LSB sections under ETF and ITF load conditions. Hence experimental studies consisting of 28 tests were first conducted in this research to assess the web crippling behaviour and strengths of LSBs under two flange load cases (ETF and ITF). Experimental web crippling capacity results were then compared with the predictions from AS/NZS 4600 and AISI S100 design rules, which showed that AS/NZS 4600 and AISI S100 design equations are very unconservative for LSBs under ETF and ITF load cases. Hence improved equations were proposed to determine the web crippling capacities of LSBs. Finite element models of the tested LSBs were then developed, and used to determine the elastic buckling loads of LSBs under ETF and ITF load cases. New equations were proposed to determine the corresponding elastic buckling coefficients of LSBs. Finally suitable design rules were also developed under the Direct Strength Method format using the test results and buckling analysis results from finite element analyses.

Electron cryo-microscopy studies of bacteriophage phi8 and archaeal virus SH1

Symmetry is a key principle in viral structures, especially the protein capsid shells. However, symmetry mismatches are very common, and often correlate with dynamic functionality of biological significance. The three-dimensional structures of two isometric viruses, bacteriophage phi8 and the archaeal virus SH1 were reconstructed using electron cryo-microscopy. Two image reconstruction methods were used: the classical icosahedral method yielded high resolution models for the symmetrical parts of the structures, and a novel asymmetric in-situ reconstruction method allowed us to resolve the symmetry mismatches at the vertices of the viruses. Evidence was found that the hexameric packaging enzyme at the vertices of phi8 does not rotate relative to the capsid. The large two-fold symmetric spikes of SH1 were found not to be responsible for infectivity. Both virus structures provided insight into the evolution of viruses. Comparison of the phi8 polymerase complex capsid with those of phi6 and other dsRNA viruses suggests that the quaternary structure in dsRNA bacteriophages differs from other dsRNA viruses. SH1 is unusual because there are two major types of capsomers building up the capsid, both of which seem to be composed mainly of single beta-barrels perpendicular to the capsid surface. This indicates that the beta-barrel may be ancestral to the double beta-barrel fold.

Synthesis, characterization, thermal degradation, and comparative chain dynamics studies of weak-link polysulfide polymers

Synthesis, spectroscopic and thermal characterization of two new classes of polysulfide polymers: poly[1(phenoxymethyl) ethylene polysulfide] (PPMEP), and poly [1-(phenoxy) ethylene polysulfide] (PPEP) is presented. The direct pyrolysis mass spectrometry (DP-MS) technique, used to study the thermal degradation behavior of these polysulfide polymers, indicated that the polymers underwent degradation through the weak-links scission. The thermal stability of the polysulfide polymers decreased as the ``rank'' (number of sulfur atoms in the polysulfide linkage; n=1, 2, 4) increased. The main-chain flexibility of these polysulfide polymers in terms of their C-13 NMR spinlattice relaxation time (T-1) measurements on the backbone methine (-CH-) and methylene (-CH2-) carbons are reported here for the first time. A comparative study of the solution chain dynamics indicated that it increased as ``rank'' of the polysulfide linkages decreased as well as by introducing side chain spacers such as, ether (-O-) or methyleneoxy (-CH2O-) groups.

X-ray photoelectron spectroscopic studies on Se/As2S3 and Sb/As2S3 nanomultilayered film

Photoinduced diffusion in Se/As2S3 and Sb/As2S3 nanomultilayered thin films are studied by X-ray photoelectron spectroscopy (XPS). The XPS measurements show the atomic movements during photoinduced diffusion in Se/As2S3 and Sb/As2S3 nanomultilayered film. The analysis of experimental data describes the nature of light induced changes indifferent structural units. (C) 2009 Elsevier B.V. All rights reserved.

In situ pump probe optical absorption studies on Sb/As2S3 nanomultilayered film

We report the in situ optical transmission change in the complete visible region of the electromagnetic spectrum to asses the kinetics of photo induced interdiffusion in Sb/As2S3 nanomultilayered film. The interdiffusion of Sb into As2S3 matrix results in the formation of Sb-As2S3 ternary solid solutions which is explained by the change in optical band gap, absorption coefficients and Tauc parameter (B-1/2) with evolution of time. The wavelength dependence of the time constants provides a better description of photo induced effects. The time evolution of the absorption coefficients and optical band gap are significantly faster in this process. (C) 2009 Elsevier B.V. All rights reserved.

Electrical Percolation studies of Polystyrene-multi wall carbon nanotubes Composites

Composites of Polystyrene-multi wall carbon nanotubes (PS-MWNTs) were prepared with loading up to 7 wt% of MWNTs by simple solvent mixing and drying technique. MWNTs with high aspect ratio similar to 4000 were used to make the polymer composites. A very high degree of dispersion of MWNTs was achieved by ultrasonication technique. As a result of high dispersion and high aspect ratio of the MWNTs electrical percolation was observed at rather low weight fraction similar to 0.0021. Characterization of the as prepared PS-MWNTs composites was done by Electron microscopy (EM), X-ray diffraction technique (XRD) and Thermogravimetery analysis (TGA).

Thermal Decomposition and Combustion Studies on Potassium Perchlorat e/Polystyrene Propellant Systems

STUDIES on potassium perchlorate/polystyrene (KP/PS) propellant systems have been carried out by using such techniques as thermogravimetry (TG), differential thermal analysis (DTA), and mass spectrometry (MS). It has been found that the thermal decomposition (TD) behavior of the KP/PS propellant is similar to that of the AP/PS propellant studied earlier.! It has also been observed that the TD of KP in the melt has a correlation with the burning rate (r) of KP/PS propellant at atmospheric pressure.