Modified conformation and physical properties in conducting polymers due to varying conjugation and solvent interactions

Small angle X-ray scattering (SAXS) studies of poly2-methoxy-5-(2'-ethyl-hexyloxy)-1,4-phenylene vinylene] (MEH-PPV) with varying conjugation, and polyethylene dioxythiophene complexed with polystyrene sulfonate (PEDOT-PSS) in different solvents have shown the importance of the role of pi-electron conjugation and solvent-chain interactions in controlling the chain conformation and assembly. In MEH-PPV, by increasing the extent of conjugation from 30 to 100%, the persistence length (l(p)) increases from 20 to 66 angstrom. Moreover, a pronounced second peak in the pair distribution function has been observed in the fully conjugated chain, at larger length scales. This feature indicates that the chain segments tend to self-assemble as the conjugation along the chain increases. In the case of PEDOT-PSS, the chains undergo solvent induced expansion and enhanced chain organization. The clusters formed by chains are better correlated in dimethyl sulfoxide (DMSO) solution than water, as observed in the scattered intensity profiles. The values of radius of gyration and the exponent (water: 2.6, DMSO: 2.31) of power-law decay, obtained from the unified scattering function (Beaucage) analysis, give evidence for chain expansion from compact (in water) to an extended coil in DMSO solutions, which is consistent with the Kratky plot analysis. The mechanism of this transition and the increase in dc conductivity of PEDOT-PSS in DMSO solution are discussed. The onset frequency for the increase in ac conduction, as well as its temperature dependence, probes the extent of the connectivity in the PEDOT-PSS system. The enhanced charge transport in PEDOT-PSS in DMSO is attributed to the extended chain conformation, as observed in the SAXS results.

Probing conformational changes in orphan nuclear receptor: The NGFI-B intermediate is a partially unfolded dimer

Human nerve growth factor-induced B (NGFI-B) is a member of the NR4A subfamily of orphan nuclear receptors (NRs). Lacking identified ligands, orphan NRs show particular co-regulator proteins binding properties, different from other NRs, and they might have a non-classical quaternary organization. A body of evidence suggests that NRs recognition of and binding to ligands, DNA, homo- and heterodimerization partners and co-regulator proteins involve significant conformational changes of the NR ligand-binding domains (LBDs). To shed light on largely unknown biophysical properties of NGFI-B, here we studied structural organization and unfolding properties of NGFI-B ligand (like)-binding domain induced by chemical perturbation. Our results show that NGFI-B LBD undergoes a two-state guanidine hydrochloride (GndHCl) induced denaturation, as judged by changes in the a-helical content of the protein monitored by circular dichroism spectroscopy (CD). In contrast, changes in the tertiary structure of NGFI-B LBD, reported by intrinsic fluorescence, reveal a clear intermediate state. Additionally, SAXS results demonstrate that the intermediate observed by intrinsic fluorescence is a partially folded homodimeric structure, which further unfolds without dissociation at higher GndHCl concentrations. This partially unfolded dimeric assembly of NGFI-B LBD might resemble an intermediate that this domain access momentarily in the native state upon interactions with functional partners. (C) 2008 Elsevier B.V. All rights reserved.

Not losing the plot : creating, collecting and curating qualitative data through a web-based application

Collecting regular personal reflections from first year teachers in rural and remote schools is challenging as they are busily absorbed in their practice, and separated from each other and the researchers by thousands of kilometres. In response, an innovative web-based solution was designed to both collect data and be a responsive support system for early career teachers as they came to terms with their new professional identities within rural and remote school settings. Using an emailed link to a web-based application named goingok.com, the participants are charting their first year plotlines using a sliding scale from ‘distressed’, ‘ok’ to ‘soaring’ and describing their self-assessment in short descriptive posts. These reflections are visible to the participants as a developing online journal, while the collections of de-identified developing plotlines are visible to the research team, alongside numerical data. This paper explores important aspects of the design process, together with the challenges and opportunities encountered in its implementation. A number of the key considerations for choosing to develop a web application for data collection are initially identified, and the resultant application features and scope are then examined. Examples are then provided about how a responsive software development approach can be part of a supportive feedback loop for participants while being an effective data collection process. Opportunities for further development are also suggested with projected implications for future research.

Anthropogenic-based regional-scale factors most consistently explain plot-level exotic diversity in grasslands

Aim Evidence linking the accumulation of exotic species to the suppression of native diversity is equivocal, often relying on data from studies that have used different methods. Plot-level studies often attribute inverse relationships between native and exotic diversity to competition, but regional abiotic filters, including anthropogenic influences, can produce similar patterns.We seek to test these alternatives using identical scale-dependent sampling protocols in multiple grasslands on two continents. Location Thirty-two grassland sites in North America and Australia. Methods We use multiscale observational data, collected identically in grain and extent at each site, to test the association of local and regional factors with the plot-level richness and abundance of native and exotic plants. Sites captured environmental and anthropogenic gradients including land-use intensity, human population density, light and soil resources, climate and elevation. Site selection occurred independently of exotic diversity, meaning that the numbers of exotic species varied randomly thereby reducing potential biases if only highly invaded sites were chosen. Results Regional factors associated directly or indirectly with human activity had the strongest associations with plot-level diversity. These regional drivers had divergent effects: urban-based economic activity was associated with high exotic : native diversity ratios; climate- and landscape-based indicators of lower human population density were associated with low exotic : native ratios. Negative correlations between plot-level native and exotic diversity, a potential signature of competitive interactions, were not prevalent; this result did not change along gradients of productivity or heterogeneity. Main conclusion We show that plot-level diversity of native and exotic plants are more consistently associatedwith regional-scale factors relating to urbanization and climate suitability than measures indicative of competition. These findings clarify the long-standing difficulty in resolving drivers of exotic diversity using single-factor mechanisms, suggesting that multiple interacting anthropogenic-based processes best explain the accumulation of exotic diversity in modern landscapes.

Determination of coefficient of consolidation from early stage of log t plot

The standard curve-fitting methods, Casagrande's log t method and Taylor's root t method, for the determination of the coefficient of consolidation use the later part of the consolidation curve and are influenced by secondary compression effects. Literature shows that secondary compression is concurrent with primary consolidation and that its effect is to decrease the value of the coefficient of consolidation. If the early part of the time-compression data is used, the values obtained will be less influenced by secondary compression effects. A method that uses the early part of the log t plot is proposed in this technical note. As the influence of secondary compression is reduced, the value obtained by this method is greater than that yielded by both the standard methods. The permeability values computed from C-v (obtained from the proposed method) rue more in agreement with the measured values than the standard methods showing that the effects of secondary compression are minimized. Time-compression data for a shorter duration is sufficient for the determination of C-v if the coefficient of secondary compression is not required.

Scaling results up from a plot and paddock scale to a property - a case study from a long-term grazing experiment in northern Australia

Grazing experiments are usually used to quantify and demonstrate the biophysical impact of grazing strategies, with the Wambiana grazing experiment being one of the longest running such experiments in northern Australia. Previous economic analyses of this experiment suggest that there is a major advantage in stocking at a fixed, moderate stocking rate or in using decision rules allowing flexible stocking to match available feed supply. The present study developed and applied a modelling procedure to use data collected at the small plot, land type and paddock scales at the experimental site to simulate the property-level implications of a range of stocking rates for a breeding-finishing cattle enterprise. The greatest economic performance was achieved at a moderate stocking rate of 10.5 adult equivalents 100 ha(-1). For the same stocking rate over time, the fixed stocking strategy gave a greater economic performance than strategies that involved moderate changes to stocking rates each year in response to feed supply. Model outcomes were consistent with previous economic analyses using experimental data. Further modelling of the experimental data is warranted and similar analyses could be applied to other major grazing experiments to allow the scaling of results to greater scales.

Plot size matters: interference from intergenotypic competition in plant phenotyping studies

Genetic and physiological studies often comprise genotypes diverse in vigour, size and flowering time. This can make the phenotyping of complex traits challenging, particularly those associated with canopy development, biomass and yield, as the environment of one genotype can be influenced by a neighbouring genotype. Limited seed and space may encourage field assessment in single, spaced rows or in small, unbordered plots, whereas the convenience of a controlled environment or greenhouse makes pot studies tempting. However, the relevance of such growing conditions to commercial field-grown crops is unclear and often doubtful. Competition for water, light and nutrients necessary for canopy growth will be variable where immediate neighbours are genetically different, particularly under stress conditions, where competition for resources and influence on productivity is greatest. Small hills and rod-rows maximise the potential for intergenotypic competition that is not relevant to a crop’s performance in monocultures. Response to resource availability will typically vary among diverse genotypes to alter genotype ranking and reduce heritability for all growth-related traits, with the possible exception of harvest index. Validation of pot experiments to performance in canopies in the field is essential, whereas the planting of multirow plots and the simple exclusion of plot borders at harvest will increase experimental precision and confidence in genotype performance in target environments.

Woody plant seedling distribution under invasive Lantana camara thickets in a dry-forest plot in Mudumalai, southern India

Lantana camara, a shrub of Central and South American origin, has become invasive across dry forests worldwide. The effect of the thicket-forming habit of L. camara as a dispersal and recruitment barrier in a community of native woody seedlings was examined in a 50-ha permanent plot located in the seasonally dry forest of Mudumalai, southern India. Sixty 100-m(2) plots were enumerated for native woody seedlings between 10-100 cm in height. Of these, 30 plots had no L. camara thickets, while the other 30 had dense thickets. The frequency of occurrence and abundance of seedlings were modelled as a function of dispersal mode (mammal, bird or mechanical) and affinities to forest habitats (dry forest, moist forest or ubiquitous) as well as presence or absence of dense L. camara thickets. Furthermore, frequency of occurrence and abundance of individual species were also compared between thickets and no L. camara. At the community level, L. camara density, dispersal mode and forest habitat affinities of species determined both frequency of occurrence and abundance of seedlings, with the abundance of dry-forest mammal-dispersed species and ubiquitous mechanically dispersed species being significantly lower under L. camara thickets. Phyllanthus emblica and Kydia calycina were found to be significantly less abundant under L. camara, whereas most other species were not affected by the presence of thickets. It was inferred that, by affecting the establishment of native tree seedlings, L. camara thickets could eventually alter the community composition of such forests.

Ramachandran plot on the web

A graphics package has been developed to display the main chain torsion angles phi, psi (phi, Psi); (Ramachandran angles) in a protein of known structure. In addition, the package calculates the Ramachandran angles at the central residue in the stretch of three amino acids having specified the flanking residue types. The package displays the Ramachandran angles along with a detailed analysis output. This software is incorporated with all the protein structures available in the Protein Databank.

Defining the ‘modified Griffin plot’ in vortex-induced vibration: revealing the effect of Reynolds number using controlled damping

In the present work, we study the transverse vortex-induced vibrations of an elastically mounted rigid cylinder in a fluid flow. We employ a technique to accurately control the structural damping, enabling the system to take on both negative and positive damping. This permits a systematic study of the effects of system mass and damping on the peak vibration response. Previous experiments over the last 30 years indicate a large scatter in peak-amplitude data ($A^*$) versus the product of mass–damping ($\alpha$), in the so-called ‘Griffin plot’. A principal result in the present work is the discovery that the data collapse very well if one takes into account the effect of Reynolds number ($\mbox{\textit{Re}}$), as an extra parameter in a modified Griffin plot. Peak amplitudes corresponding to zero damping ($A^*_{{\alpha}{=}0}$), for a compilation of experiments over a wide range of $\mbox{\textit{Re}}\,{=}\,500-33000$, are very well represented by the functional form $A^*_{\alpha{=}0} \,{=}\, f(\mbox{\textit{Re}}) \,{=}\, \log(0.41\,\mbox{\textit{Re}}^{0.36}$). For a given $\mbox{\textit{Re}}$, the amplitude $A^*$ appears to be proportional to a function of mass–damping, $A^*\propto g(\alpha)$, which is a similar function over all $\mbox{\textit{Re}}$. A good best-fit for a wide range of mass–damping and Reynolds number is thus given by the following simple expression, where $A^*\,{=}\, g(\alpha)\,f(\mbox{\textit{Re}})$: \[ A^* \,{=}\,(1 - 1.12\,\alpha + 0.30\,\alpha^2)\,\log (0.41\,\mbox{\textit{Re}}^{0.36}). \] In essence, by using a renormalized parameter, which we define as the ‘modified amplitude’, $A^*_M\,{=}\,A^*/A^*_{\alpha{=}0}$, the previously scattered data collapse very well onto a single curve, $g(\alpha)$, on what we refer to as the ‘modified Griffin plot’. There has also been much debate over the last three decades concerning the validity of using the product of mass and damping (such as $\alpha$) in these problems. Our results indicate that the combined mass–damping parameter ($\alpha$) does indeed collapse peak-amplitude data well, at a given $\mbox{\textit{Re}}$, independent of the precise mass and damping values, for mass ratios down to $m^*\,{=}\,1$.

Plot Erosion Model Using Gray Relational Analysis Method

The main factors affecting interrill erosion-including runoff discharge, rainfall intensity, mean flow velocity, and slope gradient-were analyzed by using a gray relational analysis. An equation for interrill erosion was derived by coupling this analysis with dimensional and regression analyses. The values of erosion rates predicted by this equation were in good agreement with experimental observations.

Recurrence plot analysis of DNA sequences

Recurrence plot technique of DNA sequences is established on metric representation and employed to analyze correlation structure of nucleotide strings. It is found that, in the transference of nucleotide strings, a human DNA fragment has a major correlation distance, but a yeast chromosome's correlation distance has a constant increasing. (C) 2004 Elsevier B.V All rights reserved.

Local exponential divergence plot and optimal embedding of a chaotic time-series

we propose here a local exponential divergence plot which is capable of providing a new means of characterizing chaotic time series. The suggested plot defines a time dependent exponent LAMBDA and a ''plus'' exponent LAMBDA+ which serves as a criterion for estimating simultaneously the minimal acceptable embedding dimension, the proper delay time and the largest Lyapunov exponent.