Theoretical studies on alpha-helix--DNA interactions

The interaction energies between (Ala)10 and alpha-helix fragment and different nucleotide sequences in right-handed B-form have been optimized using semi-empirical potential energy functions. The energies are calculated for two different orientations of the alpha-helix, viz., when the alpha-helix axis taken in the N----C direction is (i) parallel and (ii) antiparallel to the 5'-3' ascending strand of DNA, proximal to it. When both the DNA molecule as well as the alpha-helix are treated as rigid molecules it is found that a polyalanine alpha-helix has slightly more favourable contacts when it is in the proximity of a four nucleotide sequence of 5'-(N-A-T-N)-3' type, where N is either a purine or a pyrimidine. However, when the two interacting molecules are allowed to undergo local structural variations then the interaction energy appears to be independent of the base sequence confirming the non-specific nature of these interactions.

Elastic analysis of pin joints

The advent of large and fast digital computers and development of numerical techniques suited to these have made it possible to review the analysis of important fundamental and practical problems and phenomena of engineering which have remained intractable for a long time. The understanding of the load transfer between pin and plate is one such. Inspite of continuous attack on these problems for over half a century, classical solutions have remained limited in their approach and value to the understanding of the phenomena and the generation of design data. On the other hand, the finite element methods that have grown simultaneously with the recent development of computers have been helpful in analysing specific problems and answering specific questions, but are yet to be harnessed to assist in obtaining with economy a clearer understanding of the phenomena of partial separation and contact, friction and slip, and fretting and fatigue in pin joints. Against this background, it is useful to explore the application of the classical simple differential equation methods with the aid of computer power to open up this very important area. In this paper we describe some of the recent and current work at the Indian Institute of Science in this last direction.

Two-stage photoquenching in semi-insulating GaAs:EL2

The photoquenching of EL2 in semi‐insulating gallium arsenide is seen to be a complex process, where at low temperatures the initial slow quenching is followed by a switch to fast quenching. A possible explanation involving lattice strain mediated cooperative structural relaxation arising out of transition to the metastable state is proposed.

Inelastic dynamic response of R.C. beam column joints by using B.E.M.

A BEM formulation to obtain the inelastic response of R.C. Beam-Column joints subjected to sinusoidal loading along the boundary is presented. The equations of motion are written along with kinematical and constitutive equations. The dynamic reciprocal theorem is presented and the temporal dependence is removed by assuming steady state response.

Semi-Supervised Classification Using Sparse Gaussian Process Regression

Gaussian Processes (GPs) are promising Bayesian methods for classification and regression problems. They have also been used for semi-supervised learning tasks. In this paper, we propose a new algorithm for solving semi-supervised binary classification problem using sparse GP regression (GPR) models. It is closely related to semi-supervised learning based on support vector regression (SVR) and maximum margin clustering. The proposed algorithm is simple and easy to implement. It gives a sparse solution directly unlike the SVR based algorithm. Also, the hyperparameters are estimated easily without resorting to expensive cross-validation technique. Use of sparse GPR model helps in making the proposed algorithm scalable. Preliminary results on synthetic and real-world data sets demonstrate the efficacy of the new algorithm.

Rigid and flexible region in lysozyme and the invariant features in its hydration shell

Water-mediated transformations provide a useful handle for exploring the flexibility in protein molecules and the invariant features in their hydration shells. Low-humidity monoclinic hen egg white lysozyme, resulting from such a transformation, has perhaps the lowest solvent content observed in any protein crystal so far and has a well-ordered structure. A detailed comparison involving this structure, low-humidity tetragonal lysozyme, and the other available refined crystal structures of the enzyme permits the delineation of the relatively rigid, moderately flexible and highly flexible regions of the molecule. The relatively rigid region forms a contiguous structural unit close to the molecular centroid and encompasses parts of of the main beta-structure and three alpha-helices. The hydration shell of the protein contains 30 invariant water molecules. Many of them are involved in holding different parts of the molecule together or in stabilizing local structure. Five of the six invariant water molecules attached to the substrate-binding region form part of a water cluster contiguous with the side-chains of the catalytic residues Glu-35 and Asp-52.

Rocking response of rectangular rigid blocks under random noise base excitations

The response of a rigid rectangular block resting on a rigid foundation and acted upon simultaneously by a horizontal and a vertical random white-noise excitation is considered. In the equation of motion, the energy dissipation is modeled through a viscous damping term. Under the assumption that the body does not topple, the steady-state joint probability density function of the rotation and the rotational velocity is obtained using the Fokker-Planck equation approach. Closed form solution is obtained for a specific combination of system parameters. A more general but approximate solution to the joint probability density function based on the method of equivalent non-linearization is also presented. Further, the problem of overturning of the block is approached in the framework of the diffusion methods for first passage failure studies. The overturning of the block is deemed incipient when the response trajectories in the phase plane cross the separatrix of the conservative unforced system. Expressions for the moments of first passage time are obtained via a series solution to the governing generalized Pontriagin-Vitt equations. Numerical results illustra- tive of the theoretical solutions are presented and their validity is examined through limited amount of digital simulations.

Stress and strength analysis of pin joints in laminated anisotropic plates

Mechanical joints in composites can be tailored to achieve improved performance and better life by appropriately selecting the laminate parameters. In order to gain the best advantage of this possibility of tailoring the laminate, it is necessary to understand the influence of laminate parameters on the behaviour of joints in composites. Most of the earlier studies in this direction were based on simplified assumptions regarding load transfer at the pin-plate interface and such studies were only carried out on orthotropic and quasi-isotropic laminates. In the present study, a more rigorous analysis is carried out to study pin joints in laminates with anisotropic properties. Two types of laminates with (0/ + ?4/90)s and (0/ ± ?2/90)s layups made out of graphite epoxy T300/5208 material system are considered. The analysis mainly concentrates on clearance fit in which the pin is of smaller diameter compared to the hole. The main aspect of the analysis of pin joints is the changing contact between the pin and the plate with increasing load levels. The analysis is carried out by an iterative finite element technique and a computationally efficient routine is developed for this purpose. Numerical studies indicate that the location and magnitude of the peak stresses along the hole boundary are functions of fibre angle and the overall anisotropic properties. It is also shown that the conventional assumption of cosine distribution for the contact pressure between pin and the plate in the analysis lead to underestimation of bearing failure load and overestimation of shear and tensile failure loads in typical (0/905)s cross-ply laminates.

The status and use of tree biomass in a semi-arid village ecosystem

The status of the tree biomass resource was investigated in Ungra, a semi-arid village ecosystem in South India. There were 57 tree species with 12 trees capita−1 and 35 trees ha−1. Multiple benefit yielding local tree species dominated the village ecosystem, while fuel only or single end use trees accounted for a small proportion of trees. The standing tree biomass is adequate to meet the requirement of biomass fuels for cooking only for about two years. Village tree biomass is presently being depleted largely for export to urban areas. Tree regeneration is now characterized by transformation from multiple-use local tree species to a few single-use species. A large potential exists for tree biomass production along field boundaries (bunds), stream banks and roadsides. Biomass estimation equations were developed for 10 species.

An improved iterative finite element solution for pin joints

Accurate, reliable and economical methods of determining stress distributions are important for fastener joints. In the past the contact stress problems in these mechanically fastened joints using interference or push or clearance fit pins were solved using both inverse and iterative techniques. Inverse techniques were found to be most efficient, but at times inadequate in the presence of asymmetries. Iterative techniques based on the finite element method of analysis have wider applications, but they have the major drawbacks of being expensive and time-consuming. In this paper an improved finite element technique for iteration is presented to overcome these drawbacks. The improved iterative technique employs a frontal solver for elimination of variables not requiring iteration, by creation of a dummy element. This automatically results in a large reduction in computer time and in the size of the problem to be handled during iteration. Numerical results are compared with those available in the literature. The method is used to study an eccentrically located pin in a quasi-isotropic laminated plate under uniform tension.