DNA Free Energy-Based Promoter Prediction and Comparative Analysis of Arabidopsis and Rice Genomes

The cis-regulatory regions on DNA serve as binding sites for proteins such as transcription factors and RNA polymerase. The combinatorial interaction of these proteins plays a crucial role in transcription initiation, which is an important point of control in the regulation of gene expression. We present here an analysis of the performance of an in silico method for predicting cis-regulatory regions in the plant genomes of Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa) on the basis of free energy of DNA melting. For protein-coding genes, we achieve recall and precision of 96% and 42% for Arabidopsis and 97% and 31% for rice, respectively. For noncoding RNA genes, the program gives recall and precision of 94% and 75% for Arabidopsis and 95% and 90% for rice, respectively. Moreover, 96% of the false-positive predictions were located in noncoding regions of primary transcripts, out of which 20% were found in the first intron alone, indicating possible regulatory roles. The predictions for orthologous genes from the two genomes showed a good correlation with respect to prediction scores and promoter organization. Comparison of our results with an existing program for promoter prediction in plant genomes indicates that our method shows improved prediction capability.

MHD flow over a moving plate in a rotating fluid with magnetic field, Hall currents and free stream velocity

The non-similar boundary layer flow of a viscous incompressible electrically conducting fluid over a moving surface in a rotating fluid, in the presence of a magnetic field, Hall currents and the free stream velocity has been studied. The parabolic partial differential equations governing the flow are solved numerically using an implicit finite-difference scheme. The Coriolis force induces overshoot in the velocity profile of the primary flow and the magnetic field reduces/removes the velocity overshoot. The local skin friction coefficient for the primary flow increases with the magnetic field, but the skin friction coefficient for the secondary flow reduces it. Also the local skin friction coefficients for the primary and secondary flows are reduced due to the Hall currents. The effects of the magnetic field, Hall currents and the wall velocity, on the skin friction coefficients for the primary and secondary flows increase with the Coriolis force. The wall velocity strongly affects the flow field. When the wall velocity is equal to the free stream velocity, the skin friction coefficients for the primary and secondary flows vanish, but this does not imply separation. (C) 2002 Published by Elsevier Science Ltd.

A molecular dynamics study based post facto free energy analysis of the binding of bovine angiogenin with UMP and CMP ligands

Angiogenin is a protein belonging to the superfamily of RNase A. The RNase activity of this protein is essential for its angiogenic activity. Although members of the RNase A family carry out RNase activity, they differ markedly in their strength and specificity. In this paper, we address the problem of higher specificity of angiogenin towards cytosine against uracil in the first base binding position. We have carried out extensive nano-second level molecular dynamics(MD) computer simulations on the native bovine angiogenin and on the CMP and UMP complexes of this protein in aqueous medium with explicit molecular solvent. The structures thus generated were subjected to a rigorous free energy component analysis to arrive at a plausible molecular thermodynamic explanation for the substrate specificity of angiogenin.

Effect of absorption in aqueous and hygrothermal media on the compressive properties of glass fiber reinforced syntactic foam

Absorption due to immersion in aqueous media consisting of either saline or seawater or due to exposure to water vapor conditions and the attendant effect on the compressive properties of syntactic foam reinforced with E-glass fibers in the form of chopped strands were studied. Whereas the compressive strength decreased in samples exposed to water vapor, the saline or seawater immersed samples showed increase when compared to the dry sample. The decrease in strength in the vapor-exposed case is ascribed to higher absorption of water and to debonding and damaged features for interfaces. The enhancement of strength values for the samples immersed in saltish media is traced to the larger size of the chloride ion and resultant changes in the stress state around the fiber-bearing regions. Recourse to an analysis of scanning electron microscopic pictures of the compression-failed samples is taken to explain the observed trends.

Estimation of surface free energy of pyrites by contact angle measurements

The surface properties of coal-pyrite play a major role in determining its separation from coal in processes such as flotation. The solution pH is an important parameter in determining the surface properties of both coal and coal-pyrite such as surface free energy and zeta-potential. In the present investigation, the effect of pH on the surface free energy of pyrites from different sources was studied. The surface free energy of solids is made up of two components, i.e. the dispersive surface free energy and the acid-base interaction energy. Various methods have been used by previous researchers to evaluate these two components for different solids. In the present study, a new approach was developed and used to study the surface free energy of pyrite surfaces. Results indicate that the dispersion surface free energy of various pyrites is independent of pH while the acid-base interaction energy is strongly dependent on the pH. The acid-base interaction energy is different for each pyrite sample and also the change with pH varies with the type of pyrite. Coal-pyrite was found to be more hydrophobic than ore-pyrite which may be attributed to the presence of carbon in coal-pyrites. The acid-base interaction energy varied little with pH for coal pyrites than ore-pyrite. Comparison of acid-base interaction energy with zeta-potential measurements shows a good correlation between the minimum in acid-base interaction energy and the pHpzc.

Novel phenomenon of autoacceleration in the free radical oxidative polymerization of vinyl monomers: a thermochemical approach

A unique phenomenon of ‘autoacceleration’ was observed in a free radical polymerization of vinyl monomers and oxygen. Unlike the well known autoacceleration phenomenon in polymerization processes, this unusual phenomenon is not readily conceivable in terms of solution viscosity based reasoning. Surprisingly, we have observed manifestation of this new autoacceleration during free radical oxidative polymerization of some vinyl monomers at low conversions, where generally the polymerization reaction is zero order, the conversion–time plot are linear and viscosity effects are negligible. In the present paper, we interpret the mechanism of this new autoacceleration phenomenon on the basis of reactivity of the propagating radicals in terms of heat of formation data.

On the utility of an instrumented impact set-up to characterise the response of discontinuous buffer strips in carbon–epoxy systems in dry and wet conditions

The use of an instrumented impact test set-up to evaluate the influence of water ingress on the impact response of a carbon–epoxy (C–E) laminated composite system containing discontinuous buffer strips (BS) has been examined. The data on the BS-free C–E sample in dry conditions are used as reference to compare with the data derived from those immersed in water. The work demonstrated the utility of an instrumented impact test set-up in characterising the response, first owing to the architectural difference due to introduction of buffer strips and then due to the presence of an additional phase in the form of water ingressed into the sample. The presence of water was found to enhance the energy absorption characteristics of the C–E system with BS insertions. It was also noticed that with an increasing number of BS layer insertions, the load–time plots displayed characteristic changes. The ductility indices (DI) were found to display a lower value for the water immersed samples compared to the dry ones.

Understanding glassy dynamics from the free-energy landscape

Many interesting features of the dynamics of simple liquids near the glass transition may be understood in terms of properties of the free-energy landscape obtained from numerical studies of a model free-energy functional. Main results obtained from this approach are summarized and a list of references to relevant publications is provided. (C) 2002 Elsevier Science B.V. All rights reserved.

Carrier density-dependent transport in poly(3-methylthiophene): from injection-limited to space-charge-limited current

Current-voltage (I-V) and impedance measurements were carried out in doped poly(3-methylthiophene) devices by varying the carrier density. As the carrier concentration reduces the I-V characteristics indicate that the conduction mechanism is limited by metal-polymer interface, as also observed in impedance data. The temperature dependence of I-V in moderately doped samples shows a trap-controlled space-charge-limited conduction (SCLC); whereas in lightly doped devices injection-limited conduction is observed at lower bias and SCLC at higher voltages. The carrier density-dependent quasi-Fermi level adjustment and trap-limited transport could explain this variation in conduction mechanism. Capacitance measurements at lower frequencies and higher bias voltages show a sign change in values due to the significant variations in the relaxation behaviour for lightly and moderately doped samples. The electrical hysteresis increases as carrier density is reduced due to the time scales involved in the de-trapping of carriers.

Transition to turbulence in the free convection boundary layers on an inclined heated plate

An experimental study has been made of transition to turbulence in the free convective flows on a heated plate. Observations have been made with the plate vertical and inclined at angles up to about 50° to the vertical, both above and below the plate. A fibre anemometer was used to survey the region of intermittent turbulence. Information has thus been obtained about the range of Grashof numbers over which transition takes place. Even when the plate is vertical the region of intermittent turbulence is long. When it is inclined, this region becomes still longer in the flow below the plate as a result of the stabilizing stratification, a Richardson number effect. It is possible to have a whole flow such that it should be described as transitional, not laminar or turbulent. It was noticed that in this flow and the vertical plate one, the velocity during the laminar periods could be either of two characteristic values, one of them close to zero. The behaviour above an inclined plate could be interpreted largely as a trend towards the behaviour described in a preceding paper.

Turbulent free convection above a heated plate inclined at a small angle to the horizontal Journal

An investigation has been made of the structure of the motion above a heated plate inclined at a small angle (about 10°) to the horizontal. The turbulence is considered in terms of the similarities to and differences from the motion above an exactly horizontal surface. One effect of inclination is, of course, that there is also a mean motion. Accurate data on the mean temperature field and the intensity of the temperature fluctuations have been obtained with platinum resistance thermometers, the signals being processed electronically. More approximate information on the velocity field has been obtained with quartz fibre anemometers. These results have been supplemented qualitatively by simultaneous observations of the temperature and velocity fluctuations and also by smoke experiments. The principal features of the flow inferred from these observations are as follows. The heat transfer and the mean temperature field are not much altered by the inclination, though small, not very systematic, variations may result from the complexities of the velocity field. This supports the view that the mean temperature field is largely governed by the large-scale motions. The temperature fluctuations show a systematic variation with distance from the lower edge and resemble those above a horizontal plate when this distance is large. The largescale motions of the turbulence start close to the lower edge, but the smaller eddies do not attain full intensity until the air has moved some distance up the plate. The mean velocity receives a sizable contribution from a ‘through-flow’ between the side-walls. Superimposed on this are developments that show that the momentum transfer processes are complex and certainly not capable of representation by any simple theory such as an eddy viscosity. On the lower part of the plate there is surprisingly large acceleration, but further up the mixing action of the small eddies has a decelerating effect.

Growth and Characterization of GaAs Epitaxial Layers by MOCVD

technique, on both semi-insulating and semi-conducting CraAs substrates with (100) orientation, offset by 2° towards (110) direction. Systematic variation of As/Ga was performed to gain an understanding of growth process, type of formation and other related physical properties. The films were characterized by using the variety of techniques, such as SEM, EDAX, HRTEM, XRD, and PL. Optical and electrical properties of undoped CyaAs epilayers are presented with reference to the growth conditions and AsH3/TMGa ratio. Photoluminescence measurements of GaAs epilayers were recorded at 4.2K and shows the emission of free exciton and confirmed their high purity. The dominant residual impurities in GaAs are presented by using PL. Finally, electrochemical depth profiling exhibited almost homogeneous background carrier distribution and excellent abruptness between the thin GaAs epilayer and substrate.

Electrical and optical characterization of conducting polymers by THz time-domain spectroscopy

The absorption and index of refraction of polypyrrole (PPy) and poly-3-methylthiophene (PMeT), from low frequencies up to 4 THz, have been measured by tera-Herz (THz) time-domain spectroscopy. The complex conductance was obtained over this range of frequency. Highly conducting metallic samples follow the Drude model, whereas less conducting ones fit the localization-modified Drude model. The carrier scattering time and mobility in conducting polymers can be directly determined from these measurements.