Structural characteristics of a giant tropical liana and its mode of canopy spread in an alien environment

To circumvent the practical difficulties in research on tropical rainforest lianas in their natural habitat due to prevailing weather conditions, dense camouflaging vegetation and problems in transporting equipment for experimental investigations, Entada pursaetha DC (syn. Entada scandens Benth., Leguminosae) was grown inside a research campus in a dry subtropical environment. A solitary genet has attained a gigantic size in 17 years, infesting crowns of semi-evergreen trees growing in an area roughly equivalent to 1.6 ha. It has used aerially formed, cable-like stolons for navigating and spreading its canopy across tree gaps. Some of its parts which had remained unseen in its natural habitat due to dense vegetation are described. The attained size of this liana in a climatically different environment raises the question as to why it is restricted to evergreen rainforests. Some research problems for which this liana will be useful are pointed out.

Structural, physiological and molecular characterisation of the Australian native resurrection grass Tripogon loliiformis (F.Meull) C.E.Hubb during dehydration and rehydration

There is an urgent need to develop crops that can withstand future climates. Results from this thesis demonstrated that a native Australian resurrection grass exhibits structural, physiological and metabolic strategies to tolerate drying. These strategies may be utilized for the generation of stress tolerant crops.

Structural and Sequence Characteristics of Long alpha Helices in Globular Proteins

Elucidation of the detailed structural features and sequence requirements for iv helices of various lengths could be very important in understanding secondary structure formation in proteins and, hence. in the protein folding mechanism. An algorithm to characterize the geometry of an alpha helix from its C-alpha coordinates has been developed and used to analyze the structures of long cu helices (number of residues greater than or equal to 25) found in globular proteins, the crystal structure coordinates of which are available from the Brookhaven Protein Data Bank, Ail long a helices can be unambiguously characterized as belonging to one of three classes: linear, curved, or kinked, with a majority being curved. Analysis of the sequences of these helices reveals that the long alpha helices have unique sequence characteristics that distinguish them from the short alpha helices in globular proteins, The distribution and statistical propensities of individual amino acids to occur in long alpha heices are different from those found in short alpha helices, with amino acids having longer side chains and/or having a greater number of functional groups occurring more frequently in these helices, The sequences of the long alpha helices can be correlated with their gross structural features, i.e., whether they are curved, linear, or kinked, and in case of the curved helices, with their curvature.

On the sensitivity of elastic waves due to structural damages:Time-frequency based indexing method

Time-frequency analysis of various simulated and experimental signals due to elastic wave scattering from damage are performed using wavelet transform (WT) and Hilbert-Huang transform (HHT) and their performances are compared in context of quantifying the damages. Spectral finite element method is employed for numerical simulation of wave scattering. An analytical study is carried out to study the effects of higher-order damage parameters on the reflected wave from a damage. Based on this study, error bounds are computed for the signals in the spectral and also on the time-frequency domains. It is shown how such an error bound can provide all estimate of error in the modelling of wave propagation in structure with damage. Measures of damage based on WT and HHT is derived to quantify the damage information hidden in the signal. The aim of this study is to obtain detailed insights into the problem of (1) identifying localised damages (2) dispersion of multifrequency non-stationary signals after they interact with various types of damage and (3) quantifying the damages. Sensitivity analysis of the signal due to scattered wave based on time-frequency representation helps to correlate the variation of damage index measures with respect to the damage parameters like damage size and material degradation factors.

PocketMatch: A new algorithm to compare binding sites in protein structures

Recognizing similarities and deriving relationships among protein molecules is a fundamental requirement in present-day biology. Similarities can be present at various levels which can be detected through comparison of protein sequences or their structural folds. In some cases similarities obscure at these levels could be present merely in the substructures at their binding sites. Inferring functional similarities between protein molecules by comparing their binding sites is still largely exploratory and not as yet a routine protocol. One of the main reasons for this is the limitation in the choice of appropriate analytical tools that can compare binding sites with high sensitivity. To benefit from the enormous amount of structural data that is being rapidly accumulated, it is essential to have high throughput tools that enable large scale binding site comparison. Results: Here we present a new algorithm PocketMatch for comparison of binding sites in a frame invariant manner. Each binding site is represented by 90 lists of sorted distances capturing shape and chemical nature of the site. The sorted arrays are then aligned using an incremental alignment method and scored to obtain PMScores for pairs of sites. A comprehensive sensitivity analysis and an extensive validation of the algorithm have been carried out. A comparison with other site matching algorithms is also presented. Perturbation studies where the geometry of a given site was retained but the residue types were changed randomly, indicated that chance similarities were virtually non-existent. Our analysis also demonstrates that shape information alone is insufficient to discriminate between diverse binding sites, unless combined with chemical nature of amino acids. Conclusion: A new algorithm has been developed to compare binding sites in accurate, efficient and high-throughput manner. Though the representation used is conceptually simplistic, we demonstrate that along with the new alignment strategy used, it is sufficient to enable binding comparison with high sensitivity. Novel methodology has also been presented for validating the algorithm for accuracy and sensitivity with respect to geometry and chemical nature of the site. The method is also fast and takes about 1/250(th) second for one comparison on a single processor. A parallel version on BlueGene has also been implemented.

Structural, optical and electrical properties of sulfur-incorporated amorphous carbon films

Amorphous carbon-sulfur (a-C:S) composite films were prepared by vapor phase pyrolysis technique. The structural changes in the a-C:S films were investigated by electron microscopy. A powder X-ray diffraction (XRD) study depicts the two-phase nature of a sulfur-incorporated a-C system. The optical bandgap energy shows a decreasing trend with an increase in the sulfur content and preparation temperature. This infers a sulfur incorporation and pyrolysis temperature induced reduction in structural disorder or increase in sp (2) or pi-sites. The presence of sulfur (S 2p) in the a-C:S sample is analyzed by the X-ray photoelectron spectroscopy (XPS). The sp (3)/sp (2) hybridization ratio is determined by using the XPS C 1s peak fitting, and the results confirm an increase in sp (2) hybrids with sulfur addition to a-C. The electrical resistivity variation in the films depends on both the sulfur concentration and the pyrolysis temperature.

Structural and optical investigations of TiO2 films deposited on transparent substrates by sol-gel technique

An inexpensive and effective simple method for the preparation of nano-crystalline titanium oxide (anatase) thin films at room temperature on different transparent substrates is presented. This method is based on the use of peroxo-titanium complex, i.e. titanium isopropoxide as a single initiating organic precursor. Post-annealing treatment is necessary to convert the deposited amorphous film into titanium oxide (TiO2) crystalline (anatase) phase. These films have been characterized for X-ray diffraction (XRD) studies, atomic force microscopic (AFM) studies and optical measurements. The optical constants such as refractive index and extinction coefficient have been estimated by using envelope technique. Also, the energy gap values have been estimated using Tauc's formula for on glass and quartz substrates are found to be 3.35 eV and 3.39 eV, respectively.

Structural and optical investigation of semiconductor CdSe/CdS core-shell quantum dot thin films

Highly luminescent CdSe/CdS core-shell nanocrystals have been assembled on indium tin oxide (ITO) coated glass substrates using a wet synthesis route. The physical properties of the quantum dots (QD) have been investigated using X-ray diffraction, transmission electron microscopy and optical absorption spectroscopy techniques. These quantum dots showed a strong enhancement in the near band edge absorption. The in situ luminescence behavior has been interpreted in the light of the quantum confinement effect and induced strain in the core-shell structure.

Inverse Sensitivity Analysis of Singular Solutions of FRF matrix in Structural System Identification

The problem of structural damage detection based on measured frequency response functions of the structure in its damaged and undamaged states is considered. A novel procedure that is based on inverse sensitivity of the singular solutions of the system FRF matrix is proposed. The treatment of possibly ill-conditioned set of equations via regularization scheme and questions on spatial incompleteness of measurements are considered. The application of the method in dealing with systems with repeated natural frequencies and (or) packets of closely spaced modes is demonstrated. The relationship between the proposed method and the methods based on inverse sensitivity of eigensolutions and frequency response functions is noted. The numerical examples on a 5-degree of freedom system, a one span free-free beam and a spatially periodic multi-span beam demonstrate the efficacy of the proposed method and its superior performance vis-a-vis methods based on inverse eigensensitivity.

Structural and functional studies of Bacillus stearothermophilus serine hydroxymethyltransferase: the role of Asn(341), Tyr(60) and Phe(351) in tetrahydrofolate binding

SHMT (serine hydoxymethyltransferase), a type I pyridoxal 5'-phosphate-dependent enzyme, catalyses the conversion of L-serine and THF (tetrahydrofolate) into glycine and 5,10-methylene THE SHMT also catalyses several THF-independent side reactions such as cleavage of P-hydroxy amino acids, trans-amination, racemization and decarboxylation. In the present study, the residues Asn(341), Tyr(60) and Phe(351), which are likely to influence THF binding, were mutated to alanine, alanine and glycine respectively, to elucidate the role of these residues in THF-dependent and -independent reactions catalysed by SHMT. The N341A and Y60A bsSHMT (Bacillus stearothermophilus SHMT) mutants were inactive for the THF-dependent activity, while the mutations had no effect on THF-independent activity. However, mutation of Phe(351) to glycine did not have any effect oil either of the activities. The crystal structures of the glycine binary complexes of the mutants showed that N341A bsSHMT forms an external aldimine as in bsSHMT, whereas Y60A and F351G bsSHMTs exist as a Mixture of internal/external aldimine and gem-diamine forms. Crystal structures of all of the three Mutants obtained in the presence of L-allo-threonine were similar to the respective glycine binary complexes. The structure of the ternary complex of F351G bsSHMT with glycine and FTHF (5-formyl THF) showed that the monoglutamate side chain of FTHF is ordered in both the subunits of the asymmetric unit, unlike in the wild-type bsSHMT. The present studies demonstrate that the residues Asn(341) and Tyr(60) are pivotal for the binding of THF/FTHF, whereas Phe(351) is responsible for the asymmetric binding of FTHF in the two subunits of the dimer.

CSSP (Consensus Secondary Structure Prediction): a web-based server for structural biologists

Sequence-structure correlation studies are important in deciphering the relationships between various structural aspects, which may shed light on the protein-folding problem. The first step of this process is the prediction of secondary structure for a protein sequence of unknown three-dimensional structure. To this end, a web server has been created to predict the consensus secondary structure using well known algorithms from the literature. Furthermore, the server allows users to see the occurrence of predicted secondary structural elements in other structure and sequence databases and to visualize predicted helices as a helical wheel plot. The web server is accessible at http://bioserver1.physics.iisc.ernet.in/cssp/.

Hybrid structural control using magnetorheological dampers for base isolated structures

In this paper two nonlinear model based control algorithms have been developed to monitor the magnetorheological (MR) damper voltage. The main advantage of the proposed algorithms is that it is possible to directly monitor the voltage required to control the structural vibration considering the effect of the supplied and commanded voltage dynamics of the damper. The efficiency of the proposed techniques has been shown and compared taking an example of a base isolated three-storey building under a set of seismic excitations. Comparison of the performances with a fuzzy based intelligent control algorithm and a widely used clipped optimal strategy has also been shown.

A multiscale study on the structural and mechanical properties of the luffa sponge from Luffa cylindrica plant

Cellular materials that are often observed in biological systems exhibit excellent mechanical properties at remarkably low densities. Luffa sponge is one of such materials with a complex interconnecting porous structure. In this paper, we studied the relationship between its structural and mechanical properties at different levels of its hierarchical organization from a single fiber to a segment of whole sponge. The tensile mechanical behaviors of three single fibers were examined by an Instron testing machine and the ultrastructure of a fractured single fiber was observed in a scanning electronic microscope. Moreover, the compressive mechanical behaviors of the foam-like blocks from different locations of the sponge were examined. The difference of the compressive stress-strain responses of four sets of segmental samples were also compared. The result shows that the single fiber is a porous composite material mainly consisting of cellulose fibrils and lignin/hemicellulose matrix, and its Young's modulus and strength are comparable to wood. The mechanical behavior of the block samples from the hoop wall is superior to that from the core part. Furthermore, it shows that the influence of the inner surface on the mechanical property of the segmental sample is stronger than that of the core part; in particular, the former's Young's modulus, strength and strain energy absorbed are about 1.6 times higher. The present work can improve our understanding of the structure-function relationship of the natural material, which may inspire fabrication of new biomimetic foams with desirable mechanical efficiency for further applications in anti-crushing devices and super-light sandwich panels.

Association between biomechanical structural stresses of atherosclerotic carotid plaques and subsequent ischaemic cerebrovascular events - A longitudinal in vivo magnetic resonance imaging-based finite element study

Background: High-resolution magnetic resonance (MR) imaging has been used for MR imaging-based structural stress analysis of atherosclerotic plaques. The biomechanical stress profile of stable plaques has been observed to differ from that of unstable plaques; however, the role that structural stresses play in determining plaque vulnerability remains speculative. Methods: A total of 61 patients with previous history of symptomatic carotid artery disease underwent carotid plaque MR imaging. Plaque components of the index artery such as fibrous tissue, lipid content and plaque haemorrhage (PH) were delineated and used for finite element analysis-based maximum structural stress (M-C Stress) quantification. These patients were followed up for 2 years. The clinical end point was occurrence of an ischaemic cerebrovascular event. The association of the time to the clinical end point with plaque morphology and M-C Stress was analysed. Results: During a median follow-up duration of 514 days, 20% of patients (n=12) experienced an ischaemic event in the territory of the index carotid artery. Cox regression analysis indicated that M-C Stress (hazard ratio (HR): 12.98 (95% confidence interval (CI): 1.32-26.67, pZ0.02), fibrous cap (FC) disruption (HR: 7.39 (95% CI: 1.61e33.82), p Z 0.009) and PH (HR: 5.85 (95% CI: 1.27e26.77), p Z 0.02) are associated with the development of subsequent cerebrovascular events. Plaques associated with future events had higher M-C Stress than those which had remained asymptomatic (median (interquartile range, IQR): 330 kPa (229e494) vs. 254 kPa (166-290), p Z0.04). Conclusions: High biomechanical structural stresses, in addition to FC rupture and PH, are associated with subsequent cerebrovascular events.

Computed wall stress may predict the growth of abdominal aortic aneurysm

Growth rate of abdominal aortic aneurysm (AAA) is thought to be an important indicator of the potential risk of rupture. Wall stress is also thought to be a trigger for its rupture. However, stress change during the expansion of an AAA is unclear. Forty-four patients with AAAs were included in this longitudinal follow-up study. They were assessed by serial abdominal ultrasonography and computerized tomography (CT) scans if a critical size was reached or a rapid expansion occurred. Patient-specific 3-dimensional AAA geometries were reconstructed from the follow-up CT images. Structural analysis was performed to calculate the wall stresses of the AAA models at both baseline and final visit. A non-linear large-strain finite element method was used to compute the wall stress distribution. The average growth rate was 0.66cm/year (range 0-1.32 cm/year). A significantly positive correlation between shoulder tress at baseline and growth rate was found (r=0.342; p=0.02). A higher shoulder stress is associated with a rapidly expanding AAA. Therefore, it may be useful for estimating the growth expansion of AAAs and further risk stratification of patients with AAAs.