Combinatorial Exploration of the Structural Landscape of Acid-Pyridine Cocrystals

The structural landscape of acid-pyridine cocrystals is explored by adopting a combinatorial matrix method with 4-substituted benzoic acids and 4-substituted pyridines. The choice of the system restricts the primary synthon to the robust acid-pyridine entity. This methodology accordingly provides hints toward the formation of secondary synthons. The pK(a) rule is validated in the landscape by taking all components of the matrix together and exploring it as a whole. Along with the global features, the exploration of landscapes reveals some local features. Apart from the identification of secondary synthons, it also sheds light on the propensity of hydration in cocrystals, synthon competition, and certain topological similarities. The method described here combines two approaches, namely, database analysis and high throughput crystallography, to extract more information with minimal extra experimental effort.

GPU-based normalized cuts for road extraction using satellite imagery

This paper presents a GPU implementation of normalized cuts for road extraction problem using panchromatic satellite imagery. The roads have been extracted in three stages namely pre-processing, image segmentation and post-processing. Initially, the image is pre-processed to improve the tolerance by reducing the clutter (that mostly represents the buildings, vegetation,. and fallow regions). The road regions are then extracted using the normalized cuts algorithm. Normalized cuts algorithm is a graph-based partitioning `approach whose focus lies in extracting the global impression (perceptual grouping) of an image rather than local features. For the segmented image, post-processing is carried out using morphological operations - erosion and dilation. Finally, the road extracted image is overlaid on the original image. Here, a GPGPU (General Purpose Graphical Processing Unit) approach has been adopted to implement the same algorithm on the GPU for fast processing. A performance comparison of this proposed GPU implementation of normalized cuts algorithm with the earlier algorithm (CPU implementation) is presented. From the results, we conclude that the computational improvement in terms of time as the size of image increases for the proposed GPU implementation of normalized cuts. Also, a qualitative and quantitative assessment of the segmentation results has been projected.

Sparse coding based VLAD for efficient image retrieval

Representing images and videos in the form of compact codes has emerged as an important research interest in the vision community, in the context of web scale image/video search. Recently proposed Vector of Locally Aggregated Descriptors (VLAD), has been shown to outperform the existing retrieval techniques, while giving a desired compact representation. VLAD aggregates the local features of an image in the feature space. In this paper, we propose to represent the local features extracted from an image, as sparse codes over an over-complete dictionary, which is obtained by K-SVD based dictionary training algorithm. The proposed VLAD aggregates the residuals in the space of these sparse codes, to obtain a compact representation for the image. Experiments are performed over the `Holidays' database using SIFT features. The performance of the proposed method is compared with the original VLAD. The 4% increment in the mean average precision (mAP) indicates the better retrieval performance of the proposed sparse coding based VLAD.

Object attributes combine additively in visual search

We perceive objects as containing a variety of attributes: local features, relations between features, internal details, and global properties. But we know little about how they combine. Here, we report a remarkably simple additive rule that governs how these diverse object attributes combine in vision. The perceived dissimilarity between two objects was accurately explained as a sum of (a) spatially tuned local contour-matching processes modulated by part decomposition; (b) differences in internal details, such as texture; (c) differences in emergent attributes, such as symmetry; and (d) differences in global properties, such as orientation or overall configuration of parts. Our results elucidate an enduring question in object vision by showing that the whole object is not a sum of its parts but a sum of its many attributes.

On the computation of two-dimensional compressible flow fields by the modified local stability scheme

The modified local stability scheme is applied to several two-dimensional problems—blunt body flow, regular reflection of a shock and lambda shock. The resolution of the flow features obtained by the modified local stability scheme is found to be better than that achieved by the other first order schemes and almost identical to that achieved by the second order schemes incorporating artificial viscosity. The scheme is easy for coding, consumes moderate amount of computer storage and time. The scheme can be advantageously used in place of second order schemes.

Non local scale effects on ultrasonic wave characteristics nanorods

In this paper, the nonlocal elasticity theory has been incorporated into classical Euler-Bernoulli rod model to capture unique features of the nanorods under the umbrella of continuum mechanics theory. The strong effect of the nonlocal scale has been obtained which leads to substantially different wave behaviors of nanorods from those of macroscopic rods. Nonlocal Euler-Bernoulli bar model is developed for nanorods. Explicit expressions are derived for wavenumbers and wave speeds of nanorods. The analysis shows that the wave characteristics are highly over estimated by the classical rod model, which ignores the effect of small-length scale. The studies also shows that the nonlocal scale parameter introduces certain band gap region in axial wave mode where no wave propagation occurs. This is manifested in the spectrum cures as the region where the wavenumber tends to infinite (or wave speed tends to zero). The results can provide useful guidance for the study and design of the next generation of nanodevices that make use of the wave propagation properties of single-walled carbon nanotubes. (C) 2010 Elsevier B.V. All rights reserved.

Local structure in LaMnO3 and CaMnO3 perovskites: A quantitative structural refinement of mn K-edge XANES data

Hole-doped perovskites such as La1-xCaxMnO3 present special magnetic and magnetotransport properties, and it is commonly accepted that the local atomic structure around Mn ions plays a crucial role in determining these peculiar features. Therefore experimental techniques directly probing the local atomic structure, like x-ray absorption spectroscopy (XAS), have been widely exploited to deeply understand the physics of these compounds. Quantitative XAS analysis usually concerns the extended region [extended x-ray absorption fine structure (EXAFS)] of the absorption spectra. The near-edge region [x-ray absorption near-edge spectroscopy (XANES)] of XAS spectra can provide detailed complementary information on the electronic structure and local atomic topology around the absorber. However, the complexity of the XANES analysis usually prevents a quantitative understanding of the data. This work exploits the recently developed MXAN code to achieve a quantitative structural refinement of the Mn K-edge XANES of LaMnO3 and CaMnO3 compounds; they are the end compounds of the doped manganite series LaxCa1-xMnO3. The results derived from the EXAFS and XANES analyses are in good agreement, demonstrating that a quantitative picture of the local structure can be obtained from XANES in these crystalline compounds. Moreover, the quantitative XANES analysis provides topological information not directly achievable from EXAFS data analysis. This work demonstrates that combining the analysis of extended and near-edge regions of Mn K-edge XAS spectra could provide a complete and accurate description of Mn local atomic environment in these compounds.

The 5-Methyl Group in Thymine Dynamically Influences the Structure of A-Tracts in DNA at the Local and Global Level

DNA sequences containing a stretch of several A:T basepairs without a 5'-TA-3' step are known as A-tracts and have been the subject of extensive investigation because of their unique structural features such as a narrow minor groove and their crucial role in several biological processes. One of the aspects under investigation has been the influence of the 5-methyl group of thymine on the properties of A-tracts. Detailed molecular dynamics simulation studies of the sequences d(CGCAAAUUUGCG) and d(CGCAAATTTGCG) indicate that the presence of the 5-methyl group in thymine increases the frequency of a narrow minor groove conformation, which could facilitate its specific recognition by proteins, and reduce its susceptibility to cleavage by DNase I. The bias toward a wider minor groove in the absence of the thymine 5-methyl group is a static structural feature. Our results also indicate that the presence of the thymine 5-methyl group is necessary for calibrating the backbone conformation and the basepair and dinucleotide step geometry of the core A-tract as well as the flanking CA/TG and the neighboring GC/GC steps, as observed in free and protein-bound DNA. As a consequence, it also fine-tunes the curvature of the longer DNA fragment in which the A-tract is embedded.

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.

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.

Structural features of B-DNA dodecamer crystal structures: Influence of crystal packing versus base sequence

We have analyzed the set of inter and intra base pair parameters for each dinucleotide step in single crystal structures of dodecamers, solved at high and medium resolution and all crystallized in P2(1)2(1)2(1) space group. The objective was to identify whether all the structures which have either the Drew-Dickerson (DD) sequence d[CGCGAATTCGCG] with some base modification or related sequence (non-DD), would display the same sequence dependent structural variability about its palindromic sequence, despite the molecule being bent at one end because of similar crystal lattice packing effect. Most of the local doublet parameters for base pairs steps G2-C3 and G10-C11 positions, symmetrically situated about the lateral twofold, were significantly correlated between themselves. In non-DD sequences, significant correlations between these positional parameters were absent. The different range of local step parameter values at each sequence position contributed to the gross feature of smooth helix axis bending in all structures. The base pair parameters in some of the positions, for medium resolution DD sequence, were quite unlike the high-resolution set and encompassed a higher range of values. Twist and slide are the two main parameters that show wider conformational range for the middle region of non-DD sequence structures in comparison to DD sequence structures. On the contrary, the minor and major groove features bear good resemblance between DD and non-DD sequence crystal structure datasets. The sugar-phosphate backbone torsion angles are similar in all structures, in sharp contrast to base pair parameter variation for high and low resolution DD and non-DD sequence structures, consisting of unusual (epsilon =g(-), xi =t) B-II conformation at the 10(th) position of the dodecamer sequence. Thus examining DD and non-DD sequence structures packed in the same crystal lattice arrangement, we infer that inter and intra base pair parameters are as symmetrically equivalent in its value as the symmetry related step for the palindromic DD sequence about lateral two-fold axis. This feature would lead us to agree with the conclusion that DNA conformation is not substantially affected by end-to-end or lateral inter-molecular interaction due to crystal lattice packing effect. Non-DD sequence structures acquire step parameter values which reflect the altered sequence at each of the dodecamer sequence position in the orthorhombic lattice while showing similar gross features of DD sequence structures

RS and GIS in mapping of geomorphic records and understanding the local controls of glacial retreat from the Baspa Valley, Himachal Pradesh, India

We report here the role of remote sensing (RS) and geographical information system (GIS) in the identification of geomorphic records and understanding of the local controls on the retreat of glaciers of the Baspa Valley, Himachal Pradesh, India. The geomorphic records mapped are accumulation zone, exposed ablation zone, moraine-covered ablation zone, snout, deglaciated valley, lateral moraine, medial moraine, terminal moraine and hanging glacier. Details of these features and stages of deglaciation have been extracted from RS data and mapped in a GIS environment. Glacial geomorphic data have been generated for 22 glaciers of the Baspa Valley. The retreat of glaciers has been estimated using the glacial maxima observed on satellite images. On the basis of percentage of retreat and the critical analysis of glacial geomorphic data for 22 glaciers of the Baspa Valley, they are classified into seven categories of very low to very very high retreat. From the analysis of the above 22 glaciers, it has been found that other than global warming, the retreat of glaciers of the Baspa Valley is inversely proportional to the size of the accumulation zone and the ratio of the moraine covered ablation/exposed ablation zone.

Compressive fracture features of syntactic foams-microscopic examination

Syntactic foams made by mechanical mixing of polymeric binder and hollow spherical particles are used as core materials in sandwich structured materials. Low density of such materials makes them suitable for weight sensitive applications. The present study correlates various postcompression microscopic observations in syntactic foams to the localized events leading the material to fracture. Depending upon local stress conditions the fracture features of syntactic foam are identified for various modes of fracture such as compressive, shear and tensile. Microscopic observations were also taken at sandwich structures containing syntactic foam as core materials and also at reinforced syntactic foam containing glass fibers. These observations provide conclusive evidences for the fracture features generated under different failure modes. All the microscopic observations were taken using scanning electron microscope in secondary electron mode. (C) 2002 Kluwer Academic Publishers.

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.

Mesoporous bioactive glass and glass-ceramics: Influence of the local structure on in vitro bioactivity

Mesoporous quaternary bioactive glasses and glass-ceramic with alkali-alkaline-earth oxide were successfully synthesized by using non-ionic block copolymer P123 and evaporation induced self assembly (EISA) process followed by acid treatment assisted sal-gel method. As prepared samples has been characterized for the structural, morphological and textural properties with the various analytical techniques. Glass dissolution/ion release rate in simulated body fluid (SBF) was monitored by inductively coupled plasma (ICP) emission spectroscopy, whereas the formation of apatite phase and its crystallization at the glass and glass-ceramic surface was examined by structural, textural and microscopic probes. The influence of alkaline-earth oxide content on the glass structure followed by textural property has become more evident. The pristine glass samples exhibit a wormhole-like mesoporous structure, whereas the glass-ceramic composition is found to be in three different phases, namely crystalline hydroxyapatite, wollastonite and a residual glassy phase as observed in Cerabone (R) A/W. The existence of calcium orthophosphate phase is closely associated with the pore walls comprising nanometric-sized ``inclusions''. The observed high surface area in conjunction with the structural features provides the possible explanation for experimentally observed enhanced bioactivity through the easy access of ions to the fluid. On the other hand, presence of multiple phases in glass-ceramic sample inhibits or delays the kinetics of apatite formation. (C) 2013 Elsevier Inc. All rights reserved.