Depositional model for the early Miocene turbidite sequence, the Whakataki Formation, NZ

This research examined the influence of tectonic activity on submarine sedimentation processes, through a deposit-based analysis of turbidites in outcrop. A comprehensive field study of the Miocene Whakataki Formation yielded significant data that was analysed using methods of process-sedimentology, stratigraphy, and ichnology. Signatures of the tectonically active depositional environment were identifiable at very high resolution, from grain composition and texture to trace-fossil assemblages, as well as on a broader-scale in stratigraphic stacking patterns and structural deformation. From these results and environmental interpretations, an original facies characterisation and conceptual depositional model have been established.

Using APSIM-soiltemp to simulate soil temperature in the podding zone of peanut

Measurement or accurate simulation of soil temperature is important for improved understanding and management of peanuts (Arachis hypogaea L.), due to their geocarpic habit. A module of the Agricultural Production Systems Simulator Model (APSIM), APSIM-soiltemp, which uses input of ambient temperature, rainfall and solar radiation in conjunction with other APSIM modules, was evaluated for its ability to simulate surface 5 cm soil temperature in 35 peanut on-farm trials conducted between 2001 and 2005 in the Burnett region (25°36'S to 26°41'S, 151°39'E to 151°53'E). Soil temperature simulated by the APSIM-soiltemp module, from 30 days after sowing until maturity, closely matched the measured values (R2 ≥ 0.80)in the first three seasons (2001-04). However, a slightly poorer relationship (R2 = 0.55) between the observed and the simulated temperatures was observed in 2004-05, when the crop was severely water stressed. Nevertheless, over all the four seasons, which were characterised by a range of ambient temperature, leaf area index, radiation and soil water, each of which was found to have significant effects on soil temperature, a close 1:1 relationship (R2 = 0.85) between measured and simulated soil temperatures was observed. Therefore, the pod zone soil temperature simulated by the module can be generally relied on in place of measured input of soil temperature in APSIM applications, such as quantifying climatic risk of aflatoxin accumulation.

A kinetic model for heterogeneous acetalisation of poly(vinyl alcohol)

A model for heterogeneous acetalisation of poly(vinyl alcohol) with limited solution volume is proposed based on the grain model of Sohn and Szekely. Instead of treating the heterogeneous acetalisation as purely a diffusion process, as in the Matuzawa and Ogasawara model, the present model also takes into account the chemical reaction and the physical state of the solid polymer, such as degree of swelling and porosity, and assumes segregation of the polymer phase at higher conversion into an outer fully reacted zone and an inner zone where the reaction still proceeds. The solution of the model for limited solution volume, moreover, offers a simple method of determining the kinetic parameters and diffusivity for the solid-liquid system using the easily measurable bulk solution concentration of the liquid reactant instead of conversion-distance data for the solid phase, which are considerably more difficult to obtain.

Development of a transient gradient enhanced non local continuum damage mechanics model for masonry

Due to the advent of varied types of masonry systems a comprehensive failure mechanism of masonry essential for the understanding of its behaviour is impossible to be determined from experimental testing. As masonry is predominantly used in wall structures a biaxial stress state dominates its failure mechanism. Biaxial testing will therefore be necessary for each type of masonry, which is expensive and time consuming. A computational method would be advantageous; however masonry is complex to model which requires advanced computational modelling methods. This thesis has formulated a damage mechanics inspired modelling method and has shown that the method effectively determines the failure mechanisms and deformation characteristics of masonry under biaxial states of loading.

Chromosomal rearrangements, phenotypic variation and modularity: A case study from a contact zone between house mouse Robertsonian races in Central Italy

The Western European house mouse, Mus musculus domesticus, is well-known for the high frequency of Robertsonian fusions that have rapidly produced more than 50 karyotipic races, making it an ideal model for studying the mechanisms of chromosomal speciation. The mouse mandible is one of the traits studied most intensively to investigate the effect of Robertsonian fusions on phenotypic variation within and between populations. This complex bone structure has also been widely used to study the level of integration between different morphogenetic units. Here, with the aim of testing the effect of different karyotypic assets on the morphology of the mouse mandible and on its level of modularity, we performed morphometric analyses of mice from a contact area between two highly metacentric races in Central Italy. We found no difference in size, while the mandible shape was found to be different between the two Robertsonian races, even after accounting for the genetic relationships among individuals and geographic proximity. Our results support the existence of two modules that indicate a certain degree of evolutionary independence, but no difference in the strength of modularity between chromosomal races. Moreover, the ascending ramus showed more pronounced interpopulation/race phenotypic differences than the alveolar region, an effect that could be associated to their different polygenic architecture. This study suggests that chromosomal rearrangements play a role in the house mouse phenotypic divergence, and that the two modules of the mouse mandible are differentially affected by environmental factors and genetic makeup.

Lignin biosynthesis in Norway spruce: from a model system to the tree

Lignin is a hydrophobic polymer that is synthesised in the secondary cell walls of all vascular plants. It enables water conduction through the stem, supports the upright growth habit and protects against invading pathogens. In addition, lignin hinders the utilisation of the cellulosic cell walls of plants in pulp and paper industry and as forage. Lignin precursors are synthesised in the cytoplasm through the phenylpropanoid pathway, transported into the cell wall and oxidised by peroxidases or laccases to phenoxy radicals that couple to form the lignin polymer. This study was conducted to characterise the lignin biosynthetic pathway in Norway spruce (Picea abies (L.) Karst.). We focused on the less well-known polymerisation stage, to identify the enzymes and the regulatory mechanisms that are involved. Available data for lignin biosynthesis in gymnosperms is scarce and, for example, the latest improvements in precursor biosynthesis have only been verified in herbaceous plants. Therefore, we also wanted to study in detail the roles of individual gene family members during developmental and stress-induced lignification, using EST sequencing and real-time RT-PCR. We used, as a model, a Norway spruce tissue culture line that produces extracellular lignin into the culture medium, and showed that lignin polymerisation in the tissue culture depends on peroxidase activity. We identified in the culture medium a significant NADH oxidase activity that could generate H2O2 for peroxidases. Two basic culture medium peroxidases were shown to have high affinity to coniferyl alcohol. Conservation of the putative substrate-binding amino acids was observed when the spruce peroxidase sequences were compared with other peroxidases with high affinity to coniferyl alcohol. We also used different peroxidase fractions to produce synthetic in vitro lignins from coniferyl alcohol; however, the linkage pattern of the suspension culture lignin could not be reproduced in vitro with the purified peroxidases, nor with the full complement of culture medium proteins. This emphasised the importance of the precursor radical concentration in the reaction zone, which is controlled by the cells through the secretion of both the lignin precursors and the oxidative enzymes to the apoplast. In addition, we identified basic peroxidases that were reversibly bound to the lignin precipitate. They could be involved, for example, in the oxidation of polymeric lignin, which is required for polymer growth. The dibenzodioxocin substructure was used as a marker for polymer oxidation in the in vitro polymerisation studies, as it is a typical substructure in wood lignin and in the suspension culture lignin. Using immunolocalisation, we found the structure mainly in the S2+S3 layers of the secondary cell walls of Norway spruce tracheids. The structure was primarily formed during the late phases of lignification. Contrary to the earlier assumptions, it appears to be a terminal structure in the lignin macromolecule. Most lignin biosynthetic enzymes are encoded for by several genes, all of which may not participate in lignin biosynthesis. In order to identify the gene family members that are responsible for developmental lignification, ESTs were sequenced from the lignin-forming tissue culture and developing xylem of spruce. Expression of the identified lignin biosynthetic genes was studied using real-time RT-PCR. Candidate genes for developmental lignification were identified by a coordinated, high expression of certain genes within the gene families in all lignin-forming tissues. However, such coordinated expression was not found for peroxidase genes. We also studied stress-induced lignification either during compression wood formation by bending the stems or after Heterobasidion annosum infection. Based on gene expression profiles, stress-induced monolignol biosynthesis appeared similar to the developmental process, and only single PAL and C3H genes were specifically up-regulated by stress. On the contrary, the up-regulated peroxidase genes differed between developmental and stress-induced lignification, indicating specific responses.

Verification of the applicability of lattice model to concrete fracture by AE study

Notched three-point bend specimens (TPB) were tested under crack mouth opening displacement (CMOD) control at a rate of 0.0004 mm/s and the entire fracture process was simulated using a regular triangular two-dimensional lattice network only over the expected fracture proces zone width. The rest of the beam specimen was discretised by a coarse triangular finite element mesh. The discrete grain structure of the concrete was generated assuming the grains to be spherical. The load versus CMOD plots thus simulated agreed reasonably well with the experimental results. Moreover, acoustic emission (AE) hits were recorded during the test and compared with the number of fractured lattice elements. It was found that the cumulative AE hits correlated well with the cumulative fractured lattice elements at all load levels thus providing a useful means for predicting when the micro-cracks form during the fracturing process, both in the pre-peak and in the post-peak regimes.

A theoretical model for the magnetic helicity of solar active regions

Active regions on the solar surface are known to possess magnetic helicity, which is predominantly negative in the northern hemisphere and positive in the southern hemisphere. Choudhuri et al. [Choudhuri, A.R. On the connection between mean field dynamo theory and flux tubes. Solar Phys. 215, 31–55, 2003] proposed that the magnetic helicity arises due to the wrapping up of the poloidal field of the convection zone around rising flux tubes which form active regions. Choudhuri [Choudhuri, A.R., Chatterjee, P., Nandy, D. Helicity of solar active regions from a dynamo model. ApJ 615, L57–L60, 2004] used this idea to calculate magnetic helicity from their solar dynamo model. Apart from getting broad agreements with observational data, they also predict that the hemispheric helicity rule may be violated at the beginning of a solar cycle. Chatterjee et al. [Chatterjee, P., Choudhuri, A.R., Petrovay, K. Development of twist in an emerging magnetic flux tube by poloidal field accretion. A&A 449, 781–789, 2006] study the penetration of the wrapped poloidal field into the rising flux tube due to turbulent diffusion using a simple 1-d model. They find that the extent of penetration of the wrapped field will depend on how weak the magnetic field inside the rising flux tube becomes before its emergence. They conclude that more detailed observational data will throw light on the physical conditions of flux tubes just before their emergence to the photosphere.

A universal relation for the cohesive energy of nanoparticles

A universal relation between the cohesive energy and the particle size has been predicted based on the liquid-drop model. The universal relation is well supported by other theoretical models and the available experimental data. The universal relations for intermediate size range as well as for particles with very few atoms are discussed. A comparison of onset temperature of evaporation also establishes a universal relation.

Fracture process zone size and true fracture energy of concrete using acoustic emission

Acoustic emission (AE) energy, instead of amplitude, associated with each of the event is used to estimate the fracture process zone (FPZ) size. A steep increase in the cumulative AE energy of the events with respect to time is correlated with the formation of FPZ. Based on the AE energy released during these events and the locations of the events, FPZ size is obtained. The size-independent fracture energy is computed using the expressions given in the boundary effect model by least squares method since over-determined system of equations are obtained when data from several specimens are used. Instead of least squares method a different method is suggested in which the transition ligament length, measured from the plot of histograms of AE events plotted over the un-cracked ligament, is used directly to obtain size-independent fracture energy. The fracture energy thus calculated seems to be size-independent.

Hydrogen soil deposition and atmospheric variations in the boreal zone

This research has been prompted by an interest in the atmospheric processes of hydrogen. The sources and sinks of hydrogen are important to know, particularly if hydrogen becomes more common as a replacement for fossil fuel in combustion. Hydrogen deposition velocities (vd) were estimated by applying chamber measurements, a radon tracer method and a two-dimensional model. These three approaches were compared with each other to discover the factors affecting the soil uptake rate. A static-closed chamber technique was introduced to determine the hydrogen deposition velocity values in an urban park in Helsinki, and at a rural site at Loppi. A three-day chamber campaign to carry out soil uptake estimation was held at a remote site at Pallas in 2007 and 2008. The atmospheric mixing ratio of molecular hydrogen has also been measured by a continuous method in Helsinki in 2007 - 2008 and at Pallas from 2006 onwards. The mean vd values measured in the chamber experiments in Helsinki and Loppi were between 0.0 and 0.7 mm s-1. The ranges of the results with the radon tracer method and the two-dimensional model were 0.13 - 0.93 mm s-1 and 0.12 - 0.61 mm s-1, respectively, in Helsinki. The vd values in the three-day campaign at Pallas were 0.06 - 0.52 mm s-1 (chamber) and 0.18 - 0.52 mm s-1 (radon tracer method and two-dimensional model). At Kumpula, the radon tracer method and the chamber measurements produced higher vd values than the two-dimensional model. The results of all three methods were close to each other between November and April, except for the chamber results from January to March, while the soil was frozen. The hydrogen deposition velocity values of all three methods were compared with one-week cumulative rain sums. Precipitation increases the soil moisture, which decreases the soil uptake rate. The measurements made in snow seasons showed that a thick snow layer also hindered gas diffusion, lowering the vd values. The H2 vd values were compared to the snow depth. A decaying exponential fit was obtained as a result. During a prolonged drought in summer 2006, soil moisture values were lower than in other summer months between 2005 and 2008. Such conditions were prevailing in summer 2006 when high chamber vd values were measured. The mixing ratio of molecular hydrogen has a seasonal variation. The lowest atmospheric mixing ratios were found in the late autumn when high deposition velocity values were still being measured. The carbon monoxide (CO) mixing ratio was also measured. Hydrogen and carbon monoxide are highly correlated in an urban environment, due to the emissions originating from traffic. After correction for the soil deposition of H2, the slope was 0.49±0.07 ppb (H2) / ppb (CO). Using the corrected hydrogen-to-carbon-monoxide ratio, the total hydrogen load emitted by Helsinki traffic in 2007 was 261 t (H2) a-1. Hydrogen, methane and carbon monoxide are connected with each other through the atmospheric methane oxidation process, in which formaldehyde is produced as an important intermediate. The photochemical degradation of formaldehyde produces hydrogen and carbon monoxide as end products. Examination of back-trajectories revealed long-range transportation of carbon monoxide and methane. The trajectories can be grouped by applying cluster and source analysis methods. Thus natural and anthropogenic emission sources can be separated by analyzing trajectory clusters.

Simplified theory of carrier back-scattering in semiconducting carbon nanotubes: A Kane's model approach

We present a simplified yet analytical formulation of the carrier backscattering coefficient for zig-zag semiconducting single walled carbon nanotubes under diffusive regime. The electron-phonon scattering rate for longitudinal acoustic, optical, and zone-boundary phonon emissions for both inter- and intrasubband transition rates have been derived using Kane's nonparabolic energy subband model.The expressions for the mean free path and diffusive resistance have been formulated incorporating the aforementioned phonon scattering. Appropriate overlap function in Fermi's golden rule has been incorporated for a more general approach. The effect of energy subbands on low and high bias zones for the onset of longitudinal acoustic, optical, and zone-boundary phonon emissions and absorption have been analytically addressed. 90% transmission of the carriers from the source to the drain at 400 K for a 5 mu m long nanotube at 105 V m(-1) has been exhibited. The analytical results are in good agreement with the available experimental data. (c) 2010 American Institute of Physics.

On the momentum balance in linear-combination models for the transition zone

The momentum balance of the linear-combination integral model for the transition zone is investigated for constant pressure flows. The imbalance is found to be small enough to be negligible for all practical purposes. [S0889-504X(00)00703-0].

A multi-stage model for drop breakage in stirred vessels

Existing models for dmax predict that, in the limit of μd → ∞, dmax increases with 3/4 power of μd. Further, at low values of interfacial tension, dmax becomes independent of σ even at moderate values of μd. However, experiments contradict both the predictions show that dmax dependence on μd is much weaker, and that, even at very low values of σ,dmax does not become independent of it. A model is proposed to explain these results. The model assumes that a drop circulates in a stirred vessel along with the bulk fluid and repeatedly passes through a deformation zone followed by a relaxation zone. In the deformation zone, the turbulent inertial stress tends to deform the drop, while the viscous stress generated in the drop and the interfacial stress resist deformation. The relaxation zone is characterized by absence of turbulent stress and hence the drop tends to relax back to undeformed state. It is shown that a circulating drop, starting with some initial deformation, either reaches a steady state or breaks in one or several cycles. dmax is defined as the maximum size of a drop which, starting with an undeformed initial state for the first cycle, passes through deformation zone infinite number of times without breaking. The model predictions reduce to that of Lagisetty. (1986) for moderate values of μd and σ. The model successfully predicts the reduced dependence of dmax on μd at high values of μd as well as the dependence of dmax on σ at low values of σ. The data available in literature on dmax could be predicted to a greater accuracy by the model in comparison with existing models and correlations.

A multi-stage model for drop breakage in stirred vessels

Existing models for dmax predict that, in the limit of μd → ∞, dmax increases with 3/4 power of μd. Further, at low values of interfacial tension, dmax becomes independent of σ even at moderate values of μd. However, experiments contradict both the predictions show that dmax dependence on μd is much weaker, and that, even at very low values of σ,dmax does not become independent of it. A model is proposed to explain these results. The model assumes that a drop circulates in a stirred vessel along with the bulk fluid and repeatedly passes through a deformation zone followed by a relaxation zone. In the deformation zone, the turbulent inertial stress tends to deform the drop, while the viscous stress generated in the drop and the interfacial stress resist deformation. The relaxation zone is characterized by absence of turbulent stress and hence the drop tends to relax back to undeformed state. It is shown that a circulating drop, starting with some initial deformation, either reaches a steady state or breaks in one or several cycles. dmax is defined as the maximum size of a drop which, starting with an undeformed initial state for the first cycle, passes through deformation zone infinite number of times without breaking. The model predictions reduce to that of Lagisetty. (1986) for moderate values of μd and σ. The model successfully predicts the reduced dependence of dmax on μd at high values of μd as well as the dependence of dmax on σ at low values of σ. The data available in literature on dmax could be predicted to a greater accuracy by the model in comparison with existing models and correlations.