Inter-helical Interactions in Membrane Proteins: Analysis Based on the Local Backbone Geometry and the Side Chain Interactions

The availability of a significant number of the Structures of helical membrane proteins has prompted us to investigate the mode of helix-helix packing. In the present study, we have considered a dataset of alpha-helical membrane proteins representing Structures solved from all the known superfamilies. We have described the geometry of all the helical residues in terms of local coordinate axis at the backbone level. Significant inter-helical interactions have been considered as contacts by weighing the number of atom-atom contacts, including all the side-chain atoms. Such a definition of local axis and the contact criterion has allowed us to investigate the inter-helical interaction in a systematic and quantitative manner. We show that a single parameter (designated as alpha), which is derived from the parameters representing the Mutual orientation of local axes, is able to accurately Capture the details of helix-helix interaction. The analysis has been carried Out by dividing the dataset into parallel, anti-parallel, and perpendicular orientation of helices. The study indicates that a specific range of alpha value is preferred for interactions among the anti-parallel helices. Such a preference is also seen among interacting residues of parallel helices, however to a lesser extent. No such preference is seen in the case of perpendicular helices, the contacts that arise mainly due to the interaction Of Surface helices with the end of the trans-membrane helices. The Study Supports the prevailing view that the anti-parallel helices are well packed. However, the interactions between helices of parallel orientation are non-trivial. The packing in alpha-helical membrane proteins, which is systematically and rigorously investigated in this study, may prove to be useful in modeling of helical membrane proteins.

Consumer’s comparison between local and imported organic products: A hedonic analysis of the Japanese table wine market

Although hundreds of thousands of organic products are traded on a daily basis, it is less known how imported organic products are evaluated by consumers in an importing country. The paper analyzes Japanese wine point of sale (POS) data to examine whether consumers differentiate between local and imported organic products. The results of our hedonic analyses show that the premium for imported organic red (white) wines is about 42.996 % (8.872 %) while that for domestic red (white) organic wines is about 6.440 % (1.214 %), implying that Japanese consumers pay higher premiums for imported organic agricultural products than for those produced in Japan.

Local numerical modelling of magnetoconvection and turbulence - implications for mean-field theories

During the last decades mean-field models, in which large-scale magnetic fields and differential rotation arise due to the interaction of rotation and small-scale turbulence, have been enormously successful in reproducing many of the observed features of the Sun. In the meantime, new observational techniques, most prominently helioseismology, have yielded invaluable information about the interior of the Sun. This new information, however, imposes strict conditions on mean-field models. Moreover, most of the present mean-field models depend on knowledge of the small-scale turbulent effects that give rise to the large-scale phenomena. In many mean-field models these effects are prescribed in ad hoc fashion due to the lack of this knowledge. With large enough computers it would be possible to solve the MHD equations numerically under stellar conditions. However, the problem is too large by several orders of magnitude for the present day and any foreseeable computers. In our view, a combination of mean-field modelling and local 3D calculations is a more fruitful approach. The large-scale structures are well described by global mean-field models, provided that the small-scale turbulent effects are adequately parameterized. The latter can be achieved by performing local calculations which allow a much higher spatial resolution than what can be achieved in direct global calculations. In the present dissertation three aspects of mean-field theories and models of stars are studied. Firstly, the basic assumptions of different mean-field theories are tested with calculations of isotropic turbulence and hydrodynamic, as well as magnetohydrodynamic, convection. Secondly, even if the mean-field theory is unable to give the required transport coefficients from first principles, it is in some cases possible to compute these coefficients from 3D numerical models in a parameter range that can be considered to describe the main physical effects in an adequately realistic manner. In the present study, the Reynolds stresses and turbulent heat transport, responsible for the generation of differential rotation, were determined along the mixing length relations describing convection in stellar structure models. Furthermore, the alpha-effect and magnetic pumping due to turbulent convection in the rapid rotation regime were studied. The third area of the present study is to apply the local results in mean-field models, which task we start to undertake by applying the results concerning the alpha-effect and turbulent pumping in mean-field models describing the solar dynamo.

Medium access control schemes for local area networks with multiple priority function

This paper deals with the development and performance evaluation of three modified versions of a scheme proposed for medium access control in local area networks. The original scheme implements a collision-free and fair medium arbitration by using a control wire in conjunction with a data bus. The modifications suggested in this paper are intended to realize the multiple priority function in local area networks.

DNA polymorphism and local variation in base-pair orientation: a theoretical rationale

Basepair stacking calculations have been carried out to understand the conformational polymorphism of DNA and its sequence dependence. The recently developed self-consistent parameter set, which is specially suitable for describing irregular DNA structures, has been used to describe the geometry of a basepair doublet. While for basepairs without any propeller, the favourable stacking patterns do not appear to have very strong features, much more noticeable sequence dependent stacking patterns emerge once a propeller is applied to the basepairs. The absolute minima for most sequences occurs for a doublet geometry close to the B-DNA fibre models. Hence in the B-DNA region, no strong sequence dependent features are found, but the range of doublet geometries observed in the crystal structures generally lie within the low energy contours, obtained from stacking energy calculations. The doublet geometry corresponding to the A-DNA fibre model is not energetically favourable for the purine-pyrimidine sequences, which prefer small roll angle values when the slide has a large negative value as in A-DNA. However positive roll with large negative slide is allowed for GG, GA, AG and the pyrimidine-purine steps. This is consistent with the observed geometries of various steps in A-DNA crystals. Thus the general features of the basepair doublets predicted from these theoretical studies agree very well with the results from crystal structure analysis. However, since most sequences show an overall preference for B-type doublet geometry, the B --> A transition for random sequence DNA cannot be explained on the basis of basepair stacking interactions.

Local variability and base sequence effects in DNA crystal structures.

The importance and usefulness of local doublet parameters in understanding sequence dependent effects has been described for A- and B-DNA oligonucleotide crystal structures. Each of the two sets of local parameters described by us in the NUPARM algorithm, namely the local doublet parameters, calculated with reference to the mean z-axis, and the local helical parameters, calculated with reference to the local helix axis, is sufficient to describe the oligonucleotide structures, with the local helical parameters giving a slightly magnified picture of the variations in the structures. The values of local doublet parameters calculated by NUPARM algorithm are similar to those calculated by NEWHELIX90 program, only if the oligonucleotide fragment is not too distorted. The mean values obtained using all the available data for B-DNA crystals are not significantly different from those obtained when a limited data set is used, consisting only of structures with a data resolution of better than 2.4 A and without any bound drug molecule. Thus the variation observed in the oligonucleotide crystals appears to be independent of the quality of their crystallinity. No strong correlation is seen between any pair of local doublet parameters but the local helical parameters are interrelated by geometric relationships. An interesting feature that emerges from this analysis is that the local rise along the z-axis is highly correlated with the difference in the buckle values of the two basepairs in the doublet, as suggested earlier for the dodecamer structures (Bansal and Bhattacharyya, in Structure & Methods: DNA & RNA, Vol. 3 (Eds., R.H. Sarma and M.H. Sarma), pp. 139-153 (1990)). In fact the local rise values become almost constant for both A- and B-forms, if a correction is applied for the buckling of the basepairs. In B-DNA the AA, AT, TA and GA basepair sequences generally have a smaller local rise (3.25 A) compared to the other sequences (3.4 A) and this seems to be an intrinsic feature of basepair stacking interaction and not related to any other local doublet parameter. The roll angles in B-DNA oligonucleotides have small values (less than +/- 8 degrees), while mean local twist varies from 24 degrees to 45 degrees. The CA/TG doublet sequences show two types of preferred geometries, one with positive roll, small positive slide and reduced twist and another with negative roll, large positive slide and increased twist.(ABSTRACT TRUNCATED AT 400 WORDS)

Mapping of local electronic properties in nanostructured CMR thin films by Scanning Tunneling Microscopy (STM) and Local Conductance Map (LCMAP)

We have investigated the local electronic properties and the spatially resolved magnetoresistance of a nanostructured film of a colossal magnetoresistive (CMR) material by local conductance mapping (LCMAP) using a variable temperature Scanning Tunneling Microscope (STM) operating in a magnetic field. The nanostructured thin films (thickness ≈500nm) of the CMR material La0.67Sr0.33MnO3 (LSMO) on quartz substrates were prepared using chemical solution deposition (CSD) process. The CSD grown films were imaged by both STM and atomic force microscopy (AFM). Due to the presence of a large number of grain boundaries (GB's), these films show low field magnetoresistance (LFMR) which increases at lower temperatures. The measurement of spatially resolved electronic properties reveal the extent of variation of the density of states (DOS) at and close to the Fermi level (EF) across the grain boundaries and its role in the electrical resistance of the GB. Measurement of the local conductance maps (LCMAP) as a function of magnetic field as well as temperature reveals that the LFMR occurs at the GB. While it was known that LFMR in CMR films originates from the GB, this is the first investigation that maps the local electronic properties at a GB in a magnetic field and traces the origin of LFMR at the GB.

Relevance of local parallel theory to the linear stability of laminar separation bubbles

Laminar separation bubbles are thought to be highly non-parallel, and hence global stability studies start from this premise. However, experimentalists have always realized that the flow is more parallel than is commonly believed, for pressure-gradient-induced bubbles, and this is why linear parallel stability theory has been successful in describing their early stages of transition. The present experimental/numerical study re-examines this important issue and finds that the base flow in such a separation bubble becomes nearly parallel due to a strong-interaction process between the separated boundary layer and the outer potential flow. The so-called dead-air region or the region of constant pressure is a simple consequence of this strong interaction. We use triple-deck theory to qualitatively explain these features. Next, the implications of global analysis for the linear stability of separation bubbles are considered. In particular we show that in the initial portion of the bubble, where the flow is nearly parallel, local stability analysis is sufficient to capture the essential physics. It appears that the real utility of the global analysis is perhaps in the rear portion of the bubble, where the flow is highly non-parallel, and where the secondary/nonlinear instability stages are likely to dominate the dynamics.

On the unramified principal series of GL(3) over non-archimedean local fields

Let F be a non-archimedean local field and let O be its ring of integers. We give a complete description of the irreducible constituents of the restriction of the unramified principal series representations of GL(3)(F) to GL(3)(O). (C) 2013 Elsevier Inc. All rights reserved.

Meshless Local Petrov-Galerkin Method for Rotating Euler-Bernoulli Beam

Free vibration problem of a rotating Euler-Bernoulli beam is solved with a truly meshless local Petrov-Galerkin method. Radial basis function and summation of two radial basis functions are used for interpolation. Radial basis function satisfies the Kronecker delta property and makes it simpler to apply the essential boundary conditions. Interpolation with summation of two radial basis functions increases the node carrying capacity within the sub-domain of the trial function and higher natural frequencies can be computed by selecting the complete domain as a sub-domain of the trial function. The mass and stiffness matrices are derived and numerical results for frequencies are obtained for a fixed-free beam and hinged-free beam simulating hingeless and articulated helicopter blades. Stiffness and mass distribution suitable for wind turbine blades are also considered. Results show an accurate match with existing literature.