Conformational Dynamics in Alkyl Chains of an Anchored Bilayer: A Molecular Dynamics Study

Molecular dynamics (MD) simulations are reported for an anchored bilayer formed by the intercalation of cetyl trimethyl ammonium (CTA) and CH3(CH2)15N+(CH3) ions in a layered solid, CdPS3. The intercalated CTA ions are organized with the cationic headgroups tethered to the inorganic sheet and the hydrocarbon tails arranged as bilayers. Simulations were performed at three temperatures, 65, 180, and 298 K, using an isothermal−isobaric ensemble that was subsequently switched once macroscopic parameters had converged to a canonical isothermal−isochoric ensemble. The simulations are able to reproduce the experimental features of this system, including the formation of the bilayer and layer-to-layer separation distance. An analysis of the conformation of the chains showed that at all three temperatures a fraction of the alkyl chains retained a planar all-trans conformation, and that gauche bonds occurred as part of a “kink” (gauche+−trans−gauche−) sequence and not as isolated gauche bonds. Trans−gauche isomerization rates for the alkyl chains in the anchored bilayer are slower than those in lipid bilayers at the same temperature and show a progressive increase as the torsion numbers approach the tail. A two-dimensional periodic Voronoi tessellation analysis was performed to obtain the single-molecular area of an alkyl chain in the bilayer. The single-molecular area relaxation times are an order of magnitude longer than the trans−gauche isomerization times. The results indicate that the trans−gauche isomerization is associated with the creation and annihilation of a kink defect sequence. The results of the present MD simulation explain the apparent conflicting estimates of the gauche disorder in this system as obtained from infrared and 13C nuclear magnetic resonance measurements.

Development of a novel experimental model to investigate the influence of mechanics on bone healing

This dissertation proposed a novel experimental model combining a defect configuration with an active instrumented fixation device to investigate the influence of mechanics on bone healing. The proposed defect configuration aimed to minimise physiological loading within an experimental fracture gap and the instrumented fixator was used for the application of controlled displacements and in vivo stiffness monitoring of the healing process. This thesis has provided a novel approach to advance current knowledge and understanding of mechanobiology, which has been limited in previous experimental models.

Preliminary Phonological Analysis of Denjongka of Sikkim

This thesis is a preliminary phonological description of the Tibetan-related Denjongka language of Sikkim, India. Because the language has not been much researched and the previous studies have focused on other issues than phonology, the present paper is the first of its kind. The data for this thesis was gathered in Gangtok, the capital of Sikkim, from March to May 2004. I had four language informants from four different locations in Sikkim who spoke different dialects of Denjongka. One of the informants, from whom I recorded c. 900 words and 530 sentences, was used as the main data source for the analysis. First, I will give some ethnographic background information on the people who speak Denjongka. Next, I will discuss first the segmental and then the suprasegmental phonology of the language, which were analysed much in line with American structuralism. I also used acoustic analysis enabled by the Praat-program. Eight vowel phonemes were found. The phonemic status of /E/, however, is still suspect. I present some preliminary evidence for roundedness, frontness and height assimilation among the vowels. In the interpretation adopted in this analysis, there are no diphthongs in Denjongka. Forty consonant phonemes were found: 17 plosives, 7 affricates, 5 fricatives, 5 nasals, 4 liquids and 2 approximants. Denjongka plosives and affricates have four-way aspiration/voicing distinction: voiceless aspirated, voiceless unaspirated, voiceless slightly aspirated (devoiced), and voiced unaspirated. Two voiceless nasals and two voiceless liquids were found. Two phonation types were found to be contrastive, lax/breathy and tense/creaky. Nasalisation and length in vowels are phonemic. Denjongka is an incipient tone language. Tonal phenomena, which involve mainly pitch and phonation type, are complex. Pitch is most of the time predictable from the initial consonant and the phonation type. In some cases, however, pitch is the only contrastive feature between words. The description of Denjongka in this paper differs from the traditional four-tone system, which has been used in many descriptions of Tibetan-related languages. In the four-tone system, pitch is contrastive both in the high and low register, whereas in the present analysis pitch has been established to contrast only in the high register. Lastly, the appendices include a comparative word list of the four Denjongka dialects studied in this thesis.

Assessment of quality defects in macadamia kernels using NIR spectroscopy

Spectral data were collected of intact and ground kernels using 3 instruments (using Si-PbS, Si, and InGaAs detectors), operating over different areas of the spectrum (between 400 and 2500 nm) and employing transmittance, interactance, and reflectance sample presentation strategies. Kernels were assessed on the basis of oil and water content, and with respect to the defect categories of insect damage, rancidity, discoloration, mould growth, germination, and decomposition. Predictive model performance statistics for oil content models were acceptable on all instruments (R2 > 0.98; RMSECV < 2.5%, which is similar to reference analysis error), although that for the instrument employing reflectance optics was inferior to models developed for the instruments employing transmission optics. The spectral positions for calibration coefficients were consistent with absorbance due to the third overtones of CH2 stretching. Calibration models for moisture content in ground samples were acceptable on all instruments (R2 > 0.97; RMSECV < 0.2%), whereas calibration models for intact kernels were relatively poor. Calibration coefficients were more highly weighted around 1360, 740 and 840 nm, consistent with absorbance due to overtones of O-H stretching and combination. Intact kernels with brown centres or rancidity could be discriminated from each other and from sound kernels using principal component analysis. Part kernels affected by insect damage, discoloration, mould growth, germination, and decomposition could be discriminated from sound kernels. However, discrimination among these defect categories was not distinct and could not be validated on an independent set. It is concluded that there is good potential for a low cost Si photodiode array instrument to be employed to identify some quality defects of intact macadamia kernels and to quantify oil and moisture content of kernels in the process laboratory and for oil content in-line. Further work is required to examine the robustness of predictive models across different populations, including growing districts, cultivars and times of harvest.

Chemical bond approach to determining conductivity band gaps in amorphous chalcogenides and pnictides

The minimum energy required for the formation of conjugate pair of charged defects is found to be approximately equal to the experimental activation energy for d.c. conductivity in a number of amorphous chalcoganides and pnictides. This observation implies that the defect pair formation energy represents an intrinsic gap for transport in amorphous chalcogenides.

Blast response and failure analysis of a segmented buried tunnel

Underground tunnels are vulnerable to terrorist attacks which can cause collapse of the tunnel structures or at least extensive damage, requiring lengthy repairs. This paper treats the blast impact on a reinforced concrete segmental tunnel buried in soil under a number of parametric conditions; soil properties, soil cover, distance of explosive from the tunnel centreline and explosive weight and analyses the possible failure patterns. A fully coupled Fluid Structure Interaction (FSI) technique incorporating the Arbitrary Lagrangian-Eulerian (ALE) method is used in this study. Results indicate that the tunnel in saturated soil is more vulnerable to severe damage than that buried in either partially saturated soil or dry soil. The tunnel is also more vulnerable to surface explosions which occur directly above the centre of the tunnel than those that occur at any equivalent distances in the ground away from the tunnel centre. The research findings provide useful information on modeling, analysis, overall tunnel response and failure patterns of segmented tunnels subjected to blast loads. This information will guide future development and application of research in this field.

EPR study on the role of Mn in enhancing PTC of BaTiO3

Low concentration of Mn (< 0.05 atom%) added to lanthanide-doped ceramics for enhancing the PTC effect did not show any EPR signal due to Mn in the tetragonal phase. Above Tc (400 K) it showed the six-line signal arising from Mn2+. This is explained on the basis of Mn existing as Mn3+ ion with short relaxation time at room temperature. Oxidation state changes to Mn2+ above Tc; thus Mn3+ acts as an electron trap. This augments the function of activated defect centres (VBa /ag VBa) in diminishing the charge carrier concentration across the phase transformation.

Graphene-nanocrystalline metal sulphide composites produced by a one-pot reaction starting from graphite oxide

Graphene-nanocrystalline metal sulphide composites were prepared by a one-pot reaction. A dispersion of graphite oxide layers in an aqueous solution of metal ions (Cd2+/Zn2+) was reacted with H2S gas, which acts as a sulphide source as well as a reducing agent, resulting in the formation of metal sulphide nanoparticles and simultaneous reduction of graphite oxide sheets to graphene sheets. The surface defect related emissions shown by free metal sulphide particles are quenched in the composites due to the interaction of the surface of the nanoparticles with graphene sheets.

A comparative study of speaker adaptation methods

For the problem of speaker adaptation in speech recognition, the performance depends on the availability of adaptation data. In this paper, we have compared several existing speaker adaptation methods, viz. maximum likelihood linear regression (MLLR), eigenvoice (EV), eigenspace-based MLLR (EMLLR), segmental eigenvoice (SEV) and hierarchical eigenvoice (HEV) based methods. We also develop a new method by modifying the existing HEV method for achieving further performance improvement in a limited available data scenario. In the sense of availability of adaptation data, the new modified HEV (MHEV) method is shown to perform better than all the existing methods throughout the range of operation except the case of MLLR at the availability of more adaptation data.

Optical properties of reduced LiNbO,

Optical characteristics of H2-reduced LiNbO3 have been studied. The optical transmission in the spectral range 0.3 to 5 mu m is progressively narrowed as the sample is reduced. An absorption band centred at about 2.48 eV is assigned to small polarons. This interpretation is consistent with the published defect structure, transport and spectroscopic reports on reduced LiNbO3. A semi-quantitative analysis of the 2.48 eV absorption band is carried out by employing the Reik and Heese theory (1967) for optical properties of small polarons.

XPES studies of oxides of second- and third-row transition metals including rare earths

X-ray photoelectron spectroscopy has been employed to investigate oxides of second- and third-row transition metals, including those of rare earths. Systematics in the spin—orbit splittings and binding energies of core levels of the metals are described. In most of the cases studied, the dependence of the spin—orbit splittings on the atomic number Z is given by the relation ΔE = a(Z - Z0)4, where a is the quantum defect parameter and Z0 is the effective screening. Core-level binding energies are found to increase with the oxidation state of the metal. Most of the core-level binding energies are related to the atomic number Z by the expression E = x(Z - Z0)2, giving rise to linear plots of ln E versus ln Z. Specific features of individual oxides, with respect to satellites, multiplet structure, configuration mixing, and other properties are also discussed. The spectra of PrO2, Pr6O11, TbO2 and Tb4O7 are reported for the first time.

Identifying statutory encumbrances for seller disclosure

The standard land contracts in Queensland require a seller of land to disclose to a buyer not only registered encumbrances, but also statutory encumbrances affecting the land. Whether a statute creates a statutory encumbrance over the title to the property is therefore a key question for a seller when completing a contract. This article examines relevant case law and provides some guidelines for when a statute creates a statutory encumbrance that should be disclosed to a buyer as a defect in title.

The impact of dry matter, ripeness and internal defects on consumer perceptions of avocado quality and intentions to purchase.

Insights into the relative importance of various aspects of product quality can be provided through quantitative analysis of consumer preference and choice of fruit. In this study, methods previously used to establish taste preferences for kiwifruit (Harker et al., 2008) and conjoint approaches were used to determine the influence of three key aspects of avocado quality on consumer liking and willingness to purchase fruit: dry matter percentage (DM), level of ripeness (firmness) and internal defects (bruising). One hundred and seven consumers tasted avocados with a range of DM levels from ~20% (minimally mature) to nearly 40% (very mature), and at a range of fruit firmness (ripeness) stages (firm-ripe to soft-ripe). Responses to bruising, a common quality defect in fruit obtained from the retail shelf, were examined using a conjoint approach in which consumers were presented with photographs showing fruit affected by damage of varying severity. In terms of DM, consumers showed a progressive increase in liking and intent to buy avocados as the DM increased. In terms of ripeness, liking and purchase intent was higher in avocados that had softened to a firmness of 6.5 N or below (hand-rating 5). For internal defects, conjoint analysis revealed that price, level of bruising and incidence of bruising all significantly lowered consumers' future purchase decision, but the latter two factors had a greater impact than price. These results indicate the usefulness of the methodology, and also provide realistic targets for Hass avocado quality on the retail shelf.

MOE and MOR assessment technologies for improving graded recovery of exotic pines in Australia.

This project was designed to provide the structural softwood processing industry with the basis for improved green and dry grading to allow maximise MGP grade yields, consistent product performance and reduced processing costs. To achieve this, advanced statistical techniques were used in conjunction with state-of-the-art property measurement systems. Specifically, the project aimed to make two significant steps forward for the Australian structural softwood industry: • assessment of technologies, both existing and novel, that may lead to selection of a consistent, reliable and accurate device for the log yard and green mill. The purpose is to more accurately identify and reject material that will not make a minimum grade of MGP10 downstream; • improved correlation of grading MOE and MOR parameters in the dry mill using new analytical methods and a combination of devices. The three populations tested were stiffness-limited radiata pine, strength-limited radiata pine and Caribbean pine. Resonance tests were conducted on logs prior to sawmilling, and on boards. Raw data from existing in-line systems were captured for the green and dry boards. The dataset was analysed using classical and advanced statistical tools to provide correlations between data sets and to develop efficient strength and stiffness prediction equations. Stiffness and strength prediction algorithms were developed from raw and combined parameters. Parameters were analysed for comparison of prediction capabilities using in-line parameters, off-line parameters and a combination of in-line and off-line parameters. The results show that acoustic resonance techniques have potential for log assessment, to sort for low stiffness and/or low strength, depending on the resource. From the log measurements, a strong correlation was found between the average static MOE of the dried boards within a log and the predicted value. These results have application in segregating logs into structural and non-structural uses. Some commercial technologies are already available for this application such as Hitman LG640. For green boards it was found that in-line and laboratory acoustic devices can provide a good prediction of dry static MOE and moderate prediction for MOR.There is high potential for segregating boards at this stage of processing. Grading after the log breakdown can improve significantly the effectiveness of the mill. Subsequently, reductions in non-structural volumes can be achieved. Depending on the resource it can be expected that a 5 to 8 % reduction in non structural boards won’t be dried with an associated saving of $70 to 85/m3. For dry boards, vibration and a standard Metriguard CLT/HCLT provided a similar level of prediction on stiffness limited resource. However, Metriguard provides a better strength prediction in strength limited resources (due to this equipment’s ability to measure local characteristics). The combination of grading equipment specifically for stiffness related predictors (Metriguard or vibration) with defect detection systems (optical or X-ray scanner) provides a higher level of prediction, especially for MOR. Several commercial technologies are already available for acoustic grading on board such those from Microtec, Luxscan, Falcon engineering or Dynalyse AB for example. Differing combinations of equipment, and their strategic location within the processing chain, can dramatically improve the efficiency of the mill, the level of which will vary depending of the resource. For example, an initial acoustic sorting on green boards combined with an optical scanner associated with an acoustic system for grading dry board can result in a large reduction of the proportion of low value low non-structural produced. The application of classical MLR on several predictors proved to be effective, in particular for MOR predictions. However, the usage of a modern statistics approach(chemometrics tools) such as PLS proved to be more efficient for improving the level of prediction. Compared to existing technologies, the results of the project indicate a good improvement potential for grading in the green mill, ahead of kiln drying and subsequent cost-adding processes. The next stage is the development and refinement of systems for this purpose.

Mitochondrial Malfunction in Tumor Formation and Neuromuscular Diseases : Consequences of defects in fumarate hydratase and in the respiratory chain

The mitochondrion is an organelle of outmost importance, and the mitochondrial network performs an array of functions that go well beyond ATP synthesis. Defects in mitochondrial performance lead to diseases, often affecting nervous system and muscle. Although many of these mitochondrial diseases have been linked to defects in specific genes, the molecular mechanisms underlying the pathologies remain unclear. The work in this thesis aims to determine how defects in mitochondria are communicated within - and interpreted by - the cells, and how this contributes to disease phenotypes. Fumarate hydratase (FH) is an enzyme of the citrate cycle. Recessive defects in FH lead to infantile mitochondrial encephalopathies, while dominant mutations predispose to tumor formation. Defects in succinate dehydrogenase (SDH), the enzyme that precedes FH in the citrate cycle, have also been described. Mutations in SDH subunits SDHB, SDHC and SDHD are associated with tumor predisposition, while mutations in SDHA lead to a characteristic mitochondrial encephalopathy of childhood. Thus, the citrate cycle, via FH and SDH, seems to have essential roles in mitochondrial function, as well as in the regulation of processes such as cell proliferation, differentiation or death. Tumor predisposition is not a typical feature of mitochondrial energy deficiency diseases. However, defects in citrate cycle enzymes also affect mitochondrial energy metabolism. It is therefore necessary to distinguish what is specific for defects in citrate cycle, and thus possibly associated with the tumor phenotype, from the generic consequences of defects in mitochondrial aerobic metabolism. We used primary fibroblasts from patients with recessive FH defects to study the cellular consequences of FH-deficiency (FH-). Similarly to the tumors observed in FH- patients, these fibroblasts have very low FH activity. The use of primary cells has the advantage that they are diploid, in contrast with the aneuploid tumor cells, thereby enabling the study of the early consequences of FH- in diploid background, before tumorigenesis and aneuploidy. To distinguish the specific consequences of FH- from typical consequences of defects in mitochondrial aerobic metabolism, we used primary fibroblasts from patients with MELAS (mitochondrial encephalopathy with lactic acidosis and stroke-like episodes) and from patients with NARP (neuropathy, ataxia and retinitis pigmentosa). These diseases also affect mitochondrial aerobic metabolism but are not known to predispose to tumor formation. To study in vivo the systemic consequences of defects in mitochondrial aerobic metabolism, we used a transgenic mouse model of late-onset mitochondrial myopathy. The mouse contains a transgene with an in-frame duplication of a segment of Twinkle, the mitochondrial replicative helicase, whose defects underlie the human disease progressive external ophthalmoplegia. This mouse model replicates the phenotype in the patients, particularly neuronal degeneration, mitochondrial myopathy, and subtle decrease of respiratory chain activity associated with mtDNA deletions. Due to the accumulation of mtDNA deletions, the mouse was named deletor. We first studied the consequences of FH- and of respiratory chain defects for energy metabolism in primary fibroblasts. To further characterize the effects of FH- and respiratory chain malfunction in primary fibroblasts at transcriptional level, we used expression microarrays. In order to understand the in vivo consequences of respiratory chain defects in vivo, we also studied the transcriptional consequences of Twinkle defects in deletor mice skeletal muscle, cerebellum and hippocampus. Fumarate accumulated in the FH- homozygous cells, but not in the compound heterozygous lines. However, virtually all FH- lines lacked cytoplasmic FH. Induction of glycolysis was common to FH-, MELAS and NARP fibroblasts. In deletor muscle glycolysis seemed to be upregulated. This was in contrast with deletor cerebellum and hippocampus, where mitochondrial biogenesis was in progress. Despite sharing a glycolytic pattern in energy metabolism, FH- and respiratory chain defects led to opposite consequences in redox environment. FH- was associated with reduced redox environment, while MELAS and NARP displayed evidences of oxidative stress. The deletor cerebellum had transcriptional induction of antioxidant defenses, suggesting increased production of reactive oxygen species. Since the fibroblasts do not represent the tissues where the tumors appear in FH- patients, we compared the fibroblast array data with the data from FH- leiomyomas and normal myometrium. This allowed the determination of the pathways and networks affected by FH-deficiency in primary cells that are also relevant for myoma formation. A key pathway regulating smooth muscle differentiation, SRF (serum response factor)-FOS-JUNB, was found to be downregulated in FH- cells and in myomas. While in the deletor mouse many pathways were affected in a tissue-specific basis, like FGF21 induction in the deletor muscle, others were systemic, such as the downregulation of ALAS2-linked heme synthesis in all deletor tissues analyzed. However, interestingly, even a tissue-specific response of FGF21 excretion could elicit a global starvation response. The work presented in this thesis has contributed to a better understanding of mitochondrial stress signalling and of pathways interpreting and transducing it to human pathology.