Recognition of Interaction Interface Residues in Low-Resolution Structures of Protein Assemblies Solely from the Positions of C alpha Atoms

Background: The number of available structures of large multi-protein assemblies is quite small. Such structures provide phenomenal insights on the organization, mechanism of formation and functional properties of the assembly. Hence detailed analysis of such structures is highly rewarding. However, the common problem in such analyses is the low resolution of these structures. In the recent times a number of attempts that combine low resolution cryo-EM data with higher resolution structures determined using X-ray analysis or NMR or generated using comparative modeling have been reported. Even in such attempts the best result one arrives at is the very course idea about the assembly structure in terms of trace of the C alpha atoms which are modeled with modest accuracy. Methodology/Principal Findings: In this paper first we present an objective approach to identify potentially solvent exposed and buried residues solely from the position of C alpha atoms and amino acid sequence using residue type-dependent thresholds for accessible surface areas of C alpha. We extend the method further to recognize potential protein-protein interface residues. Conclusion/Significance: Our approach to identify buried and exposed residues solely from the positions of C alpha atoms resulted in an accuracy of 84%, sensitivity of 83-89% and specificity of 67-94% while recognition of interfacial residues corresponded to an accuracy of 94%, sensitivity of 70-96% and specificity of 58-94%. Interestingly, detailed analysis of cases of mismatch between recognition of interface residues from C alpha positions and all-atom models suggested that, recognition of interfacial residues using C alpha atoms only correspond better with intuitive notion of what is an interfacial residue. Our method should be useful in the objective analysis of structures of protein assemblies when positions of only C alpha positions are available as, for example, in the cases of integration of cryo-EM data and high resolution structures of the components of the assembly.

Geometric Representation of Graphs in Low Dimension Using Axis Parallel Boxes

An axis-parallel k-dimensional box is a Cartesian product R-1 x R-2 x...x R-k where R-i (for 1 <= i <= k) is a closed interval of the form [a(i), b(i)] on the real line. For a graph G, its boxicity box(G) is the minimum dimension k, such that G is representable as the intersection graph of (axis-parallel) boxes in k-dimensional space. The concept of boxicity finds applications in various areas such as ecology, operations research etc. A number of NP-hard problems are either polynomial time solvable or have much better approximation ratio on low boxicity graphs. For example, the max-clique problem is polynomial time solvable on bounded boxicity graphs and the maximum independent set problem for boxicity d graphs, given a box representation, has a left perpendicular1 + 1/c log n right perpendicular(d-1) approximation ratio for any constant c >= 1 when d >= 2. In most cases, the first step usually is computing a low dimensional box representation of the given graph. Deciding whether the boxicity of a graph is at most 2 itself is NP-hard. We give an efficient randomized algorithm to construct a box representation of any graph G on n vertices in left perpendicular(Delta + 2) ln nright perpendicular dimensions, where Delta is the maximum degree of G. This algorithm implies that box(G) <= left perpendicular(Delta + 2) ln nright perpendicular for any graph G. Our bound is tight up to a factor of ln n. We also show that our randomized algorithm can be derandomized to get a polynomial time deterministic algorithm. Though our general upper bound is in terms of maximum degree Delta, we show that for almost all graphs on n vertices, their boxicity is O(d(av) ln n) where d(av) is the average degree.

Multistation study of nighttime scintillations in low latitudes: Evidence of control by equatorial F region irregularities

VHF nighttime scintillations, recorded during a high solar activity period at a meridian chain of stations covering a magnetic latitude belt of 3°–21°N (420 km subionospheric points) are analyzed to investigate the influence of equatorial spread F irregularities on the occurrence of scintillation at latitudes away from the equator. Observations show that saturated amplitude scintillations start abruptly about one and a half hours after ground sunset and their onset is almost simultaneous at stations whose subionospheric points are within 12°N latitude of the magnetic equator, but is delayed at a station whose subionospheric point is at 21°N magnetic latitude by 15 min to 4 hours. In addition, the occurrence of postsunset scintillations at all the stations is found to be conditional on their prior occurrence at the equatorial station. If no postsunset scintillation activity is seen at the equatorial station, no scintillations are seen at other stations also. The occurrence of scintillations is explained as caused by rising plasma bubbles and associated irregularities over the magnetic equator and the subsequent mapping of these irregularities down the magnetic field lines to the F region of higher latitudes through some instantaneous mechanism; and hence an equatorial control is established on the generation of postsunset scintillation-producing irregularities in the entire low-latitude belt.

Analysis of shore line protection works in tsunami hit areas of east coast of India

Evaluation and design of shore protection works in the case of tsunamis assumes considerable importance in view of the impact it had in the recent tsunami of 26th December 2004 in India and other countries in Asia. The fact that there are no proper guidelines have made in the matters worse and resulted in the magnitude of damage that occurred. Survey of the damages indicated that the scour as a result of high velocities is one of the prime reasons for damages in the case of simple structures. It is revealed that sea walls in some cases have been helpful to minimize the damages. The objective of this paper is to suggest that design of shore line protection systems using expected wave heights that get generated and use of flexible systems such as geocells is likely to give a better protection. The protection systems can be designed to withstand the wave forces that corresponding to different probabilities of incidence. A design approach of geocells protection system is suggested and illustrated with reference to the data of wave heights in the east coast of India.

Kinetic approach to dislocation bending in low-mobility films

A kinetic model has been developed for dislocation bending at the growth surface in compressively stressed low-mobility films such as III-V nitrides. It is based on a reduction in the number of atoms at the growth surface. Stress and nonstress sources of driving force for such a reduction are discussed. A comparison between the derived equations and experimentally measured stress evolution data yields good agreement between the predicted and observed angles through which dislocations bend.

Regionalization of precipitation in data sparse areas using large scale atmospheric variables - A fuzzy clustering approach

Delineation of homogeneous precipitation regions (regionalization) is necessary for investigating frequency and spatial distribution of meteorological droughts. The conventional methods of regionalization use statistics of precipitation as attributes to establish homogeneous regions. Therefore they cannot be used to form regions in ungauged areas, and they may not be useful to form meaningful regions in areas having sparse rain gauge density. Further, validation of the regions for homogeneity in precipitation is not possible, since the use of the precipitation statistics to form regions and subsequently to test the regional homogeneity is not appropriate. To alleviate this problem, an approach based on fuzzy cluster analysis is presented. It allows delineation of homogeneous precipitation regions in data sparse areas using large scale atmospheric variables (LSAV), which influence precipitation in the study area, as attributes. The LSAV, location parameters (latitude, longitude and altitude) and seasonality of precipitation are suggested as features for regionalization. The approach allows independent validation of the identified regions for homogeneity using statistics computed from the observed precipitation. Further it has the ability to form regions even in ungauged areas, owing to the use of attributes that can be reliably estimated even when no at-site precipitation data are available. The approach was applied to delineate homogeneous annual rainfall regions in India, and its effectiveness is illustrated by comparing the results with those obtained using rainfall statistics, regionalization based on hard cluster analysis, and meteorological sub-divisions in India. (C) 2011 Elsevier B.V. All rights reserved.

Recent Advances in Low CTE and High Density System-on-a-Package (SOP) Substrate with Thin Film Component Integration

The Packaging Research Center has been developing next generation system-on-a-package (SOP) technology with digital, RF, optical, and sensor functions integrated in a single package/module. The goal of this effort is to develop a platform substrate technology providing very high wiring density and embedded thin film passive and active components using PWB compatible materials and processes. The latest SOP baseline process test vehicle has been fabricated on novel Si-matched CTE, high modulus C-SiC composite core substrates using 10mum thick BCB dielectric films with loss tangent of 0.0008 and dielectric constant of 2.65. A semi-additive plating process has been developed for multilayer microvia build-up using BCB without the use of any vacuum deposition or polishing/CMP processes. PWB and package substrate compatible processes such as plasma surface treatment/desmear and electroless/electrolytic pulse reverse plating was used. The smallest line width and space demonstrated in this paper is 6mum with microvia diameters in the 15-30mum range. This build-up process has also been developed on medium CTE organic laminates including MCL-E-679F from Hitachi Chemical and PTFE laminates with Cu-Invar-Cu core. Embedded decoupling capacitors with capacitance density of >500nF/cm2 have been integrated into the build-up layers using sol-gel synthesized BaTiO3 thin films (200-300nm film thickness) deposited on copper foils and integrated using vacuum lamination and subtractive etch processes. Thin metal alloy resistor films have been integrated into the SOP substrate using two methods: (a) NiCrAlSi thin films (25ohms per square) deposited on copper foils (Gould Electronics) laminated on the build-up layers and two step etch process for resistor definition, and (b) electroless plated Ni-W-P thin films (70 ohms to few Kohms per square) on the BCB dielectric by plasma surface treatment and activation. The electrical design and build-up layer structure along- - with key materials and processes used in the fabrication of the SOP4 test vehicle were presented in this paper. Initial results from the high density wiring and embedded thin film components were also presented. The focus of this paper is on integration of materials, processes and structures in a single package substrate for system-on-a-package (SOP) implementation

Geometric representations of graphs in low dimension

We give an efficient randomized algorithm to construct a box representation of any graph G on n vertices in $1.5 (\Delta + 2) \ln n$ dimensions, where $\Delta$ is the maximum degree of G. We also show that $\boxi(G) \le (\Delta + 2) \ln n$ for any graph G. Our bound is tight up to a factor of $\ln n$. We also show that our randomized algorithm can be derandomized to get a polynomial time deterministic algorithm. Though our general upper bound is in terms of maximum degree $\Delta$, we show that for almost all graphs on n vertices, its boxicity is upper bound by $c\cdot(d_{av} + 1) \ln n$ where d_{av} is the average degree and c is a small constant. Also, we show that for any graph G, $\boxi(G) \le \sqrt{8 n d_{av} \ln n}$, which is tight up to a factor of $b \sqrt{\ln n}$ for a constant b.

DEPRESSION OF MAGNETlCALLY FIXED EMISSION ZONE IN LOW PRESSURE MERCURY ARCS

A transverse magnetic field was used to fix the cathode spot of a low pressure mercury arc with liquid cathode It was noticed that such fixation causes consider-abledepression of the emission zone below the mercury level.This depression varies with the arc current and the magnetic field and is associated with an increase in the arc voltage drop. It indicates appreciable pressure in the emission zone.

Suppression of gravitational instabilities by dominant dark matter halo in low-surface-brightness galaxies

The low-surface-brightness galaxies are gas rich and yet have a low star formation rate; this is a well-known puzzle. The spiral features in these galaxies are weak and difficult to trace, although this aspect has not been studied much. These galaxies are known to be dominated by the dark matter halo from the innermost regions. Here, we do a stability analysis for the galactic disc of UGC 7321, a low-surface-brightness, superthin galaxy, for which the various observational input parameters are available. We show that the disc is stable against local, linear axisymmetric and non-axisymmetric perturbations. The Toomre Q parameter values are found to be large (>> 1) mainly due to the low disc surface density, and the high rotation velocity resulting due to the dominant dark matter halo, which could explain the observed low star formation rate. For the stars-alone case, the disc shows finite swing amplification but the addition of dark matter halo suppresses that amplification almost completely. Even the inclusion of the low-dispersion gas which constitutes a high disc mass fraction does not help in causing swing amplification. This can explain why these galaxies do not show strong spiral features. Thus, the dynamical effect of a halo that is dominant from inner regions can naturally explain why star formation and spiral features are largely suppressed in low-surface-brightness galaxies, making these different from the high-surface-brightness galaxies.

Effect of morphology on electrical treeing in low density polyethylene nanocomposites

Influence of polymer morphology on the inception and the growth of electrical trees in unfilled low density polyethylene (LDPE) as well as LDPE filled with 1, 3 and 5% by weight nanoalumina samples stressed with 50 Hz ac voltage has been studied. It is seen that there is a significant improvement in tree inception voltage with filler loading in LDPE filled with nanoparticles. Tree inception voltage increased with the filler loading up to 3% by weight nanoalumina loading and showed a reduction at 5% by weight loading. Change in tree growth patterns from branch to bush as well as a slower tree growth with increase in filler loading in LDPE alumina nanocomposites were observed. The degree of crystallinity and change in crystalline morphology induced by the presence of alumina nanoparticles in LDPE was studied using differential scanning calorimetry (DSC) and scanning electron microscopy (SEM). DSC results show a similar melting behaviour for both unfilled LDPE and LDPE nanocomposites. However, there is a reduction in the degree of crystallinity for LDPE filled with 5% by weight nanoalumina. An increase in lamellae packing with increase in filler loadings and a highly disordered spherulitic structure for LDPE filled with 5% by weight nanoalumina was observed from the SEM images. The slow propagation of tree growth as well as reduction in tree inception voltage with increase in filler loadings were attributed to the morphological changes observed in the LDPE nanocomposites.

The influence of mesoporous silica in low T-g cyclic olefin copolymer nanocomposite films: Mechanical and moisture barrier studies

In this study, mesoporous silica-cyclic olefin copolymer nanocomposite films were fabricated by solution casting. With an increase in silica loading, the stiffness of the matrix increased. The nanocomposite film shows increased strain to failure with moisture after aging by matrix plasticization. The storage modulus and loss factor for samples with silica content show better results compared with pristine polymer, as indicated by dynamic mechanical analysis. The interaction between filler-polymer chain exhibit hydrophobicity compared to the neat polymer. Water absorption studies at room temperature and near the T-g of the polymer (similar to 64 degrees C) were carried out. The nanocomposites up to 4 wt% filler reduces the water diffusion by forming hydrogen and chemical bonding. The result by calcium degradation test method for moisture permeability and Schottky structured organic device encapsulation under weathering condition confirms the effective reinforcement effect of silica particles in the matrix. (C) 2014 Elsevier Ltd. All rights reserved.