Theoretical calculations of base-base interactions in nucleic acids: I Stacking interactions in free bases

Stacking interactions in free bases were computed on the basis of molecular association. The results of the calculations were compared with the stacking patterns observed in a few single crystals of nucleic acid components as examples. The following are the conclusions: (i) there can be two types of stacking pattern classified as normal and inverted types for any two interacting bases and both can be energetically favourable (ii) in both the types the stacking interaction is a combined effect of the overlap of the interacting bases and relative positions and orientations of the atomic centres of the two bases (iii) crystal symmetry and H-bonding interaction may influence stacking patterns.

Relative stability of DNA as a generic criterion for promoter prediction: whole genome annotation of microbial genomes with varying nucleotide base composition

The rapid increase in genome sequence information has necessitated the annotation of their functional elements, particularly those occurring in the non-coding regions, in the genomic context. Promoter region is the key regulatory region, which enables the gene to be transcribed or repressed, but it is difficult to determine experimentally. Hence an in silico identification of promoters is crucial in order to guide experimental work and to pin point the key region that controls the transcription initiation of a gene. In this analysis, we demonstrate that while the promoter regions are in general less stable than the flanking regions, their average free energy varies depending on the GC composition of the flanking genomic sequence. We have therefore obtained a set of free energy threshold values, for genomic DNA with varying GC content and used them as generic criteria for predicting promoter regions in several microbial genomes, using an in-house developed tool `PromPredict'. On applying it to predict promoter regions corresponding to the 1144 and 612 experimentally validated TSSs in E. coli (50.8% GC) and B. subtilis (43.5% GC) sensitivity of 99% and 95% and precision values of 58% and 60%, respectively, were achieved. For the limited data set of 81 TSSs available for M. tuberculosis (65.6% GC) a sensitivity of 100% and precision of 49% was obtained.

NUVIEW:software for display and interactive manipulation of nucleic acid models

The NUVIEW software package allows skeletal models of any double helical nucleic acid molecule to be displayed out a graphics monitor and to apply various rotations, translations and scaling transformations interactively, through the keyboard. The skeletal model is generated by connecting any pair of representative points, one from each of the bases in the basepair. In addition to the above mentioned manipulations, the base residues can be identified by using a locator and the distance between any pair of residues can be obtained. A sequence based color coded display allows easy identification of sequence repeats, such as runs of Adenines. The real time interactive manipulation of such skeletal models for large DNA/RNA double helices, can be used to trace the path of the nucleic acid chain in three dimensions and hence get a better idea of its topology, location of linear or curved regions, distances between far off regions in the sequence etc. A physical picture of these features will assist in understanding the relationship between base sequence, structure and biological function in nucleic acids.

Two highly unsymmetrical tetradentate (N3O) Schiff base copper(II) complexes: Template synthesis, structural characterization, magnetic and computational studies

Two new copper(II) complexes, [Cu-2(L-1)(2)](ClO4)(2) (1) and [Cu(L-2)(ClO4)] (2), of the highly unsymmetrical tetradentate (N3O) Schiff base ligands HL1 and HL2 (where HL1 = N-(2-hydroxyacetophenone)-bis-3-aminopropylamine and HL2 = N-(salicyldehydine)-bis-3-aminopropylamine) have been synthesised using a template method. Their single crystal X-ray structures show that in complex 1 two independent copper(II) centers are doubly bridged through sphenoxo-O atoms (O1A and O1B) of the two ligands and each copper atom is five-coordinated with a distorted square pyramidal geometry. The asymmetric unit of complex 2 consists of two crystallographically independe N-(salicylidene) bis(aminopropyl)amine-copper(II) molecules, A and B, with similar square pyramidal geometries. Cryomagnetic susceptibility measurements (5-300 K) on complex 1 reveal a distinct antiferromagnetic interaction with J=-23.6 cm(-1), which is substantiated by a DFT calculation (J=-27.6 cm(-1)) using the B3LYP functional. Complex 1, immobilized over highly ordered hexagonal mesoporous silica, shows moderate catalytic activity for the epoxidation of cyclohexene and styrene in the presence of TBHP as an oxidant.

Synthesis of liquid crystalline benzothiazole base derivatives: A study of their optical and electrical properties

Two new donor-acceptor type liquid crystalline semiconductors based on benzothiazole have been synthesized. Their structural, photophysical and electronic properties were investigated using X-ray diffraction, atomic force microscopy, cyclic voltammetry, UV-Vis, photoluminescence, and Raman spectroscopy. The liquid crystalline behaviour of the molecules was thoroughly examined by differential scanning calorimetry (DSC) and optical polarizing microscope. The DSC and thermogravimetric analysis (TGA) show that these materials posses excellent thermal stability and have decomposition temperatures in excess of 300 degrees C. Beyond 160 degrees C both molecules show a smectic A liquid crystalline phase that exists till about 240 degrees C. Field-effect transistors were fabricated by vacuum evaporating the semiconductor layer using standard bottom gate/top contact geometry. The devices exhibit p-channel behaviour with hole mobilities of 10(-2) cm(2)/Vs. (C) 2009 Elsevier B.V. All rights reserved.

Anion directed template synthesis of Cu(II) complexes of a N,N,O donor mono-condensed Schiff base ligand: A molecular scaffold forming highly ordered H-bonded rectangular grids

Anion directed, template syntheses of two dinuclear copper(II) complexes of mono-condensed Schiff base ligand Hdipn (4-[(3-aminopentylimino)-methyl]-benzene-1,3-diol) involving 2,4- dihydroxybenzaldehyde and 1,3-diaminopentane were realized in the presence of bridging azide and acetate anions. Both complexes, [Cu-2(dipn)(2)(N-3)(2)] (1) and [Cu-2(dip(n))(2)(OAc)(2)] (2) have been characterized by X-ray crystallography. The two mononuclear units are joined together by basal-apical, double end-on azido bridges in complex 1 and by basal-apical, double mono-atomic acetate oxygen-bridges in 2. Both complexes form rectangular grid-like supramolecular structures via H-bonds connecting the azide or acetate anion and the p-hydroxy group of 2,4- dihydroxybenzaldehyde. Variable-temperature (300-2 K) magnetic susceptibility measurements reveal that complex 1 has antiferromagnetic coupling (J = -2.10 cm (1)) through the azide bridge while 2 has intra-dimer ferromagnetic coupling through the acetate bridge and inter-dimer antiferromagnetic coupling through H-bonds (J = 2.85 cm (1), J' = -1.08 cm (1)). (C) 2009 Elsevier B. V. All rights reserved.

Iron(III) Schiff base complexes of arginine and lysine as netropsin mimics showing AT-selective DNA binding and photonuclease activity

Iron(III) complexes [Fe(L)(2)]Cl (1-3), where L is monoanionic N-salicylidene-arginine (sal-argH for 1), hydroxynaphthylidene-arginine (nap-argH for 2) and N-salicylidene-lysine (sal-lysH for 3), were prepared and their DNA binding and photo-induced DNA cleavage activity studied. Complex 3 as its hexafluorophosphate salt [Fe(sal-lysH)(2)](PF6)center dot 6H(2)O (3a) was structurally characterized by single crystal Xray crystallography. The crystals belonged to the triclinic space group P-1. The complex has two tridentate ligands in FeN2O4 coordination geometry with two pendant cationic amine moieties. Complexes 1 and 2 with two pendant cationic guanidinium moieties are the structural models for the antitumor antibiotics netropsin. The complexes are stable and soluble in water. They showed quasi-reversible Fe(III)/Fe(II) redox couple near 0.6 V in H2O-0.1 M KCl. The high-spin 3d(5)-iron(III) complexes with mu(eff) value of similar to 5.9 mu(B) displayed ligand-to-metal charge transfer electronic band near 500 mm in Tris-HCl buffer. The complexes show binding to Calf Thymus (CT) DNA. Complex 2 showed better binding propensity to the synthetic oligomer poly(dA)center dot poly(dT) than to CT-DNA or poly(dG)center dot poly(dC). All the complexes displayed chemical nuclease activity in the presence of 3-mercaptopropionic acid as a reducing agent and cleaved supercoiled pUC19 DNA to its nicked circular form. They exhibited photo-induced DNA cleavage activity in UV-A light and visible light via a mechanistic pathway that involves the formation of reactive hydroxyl radical species. (C) 2010 Elsevier Inc. All rights reserved.

Design of plane sand-bed channels affected by seepage

The importance of seepage in the design of channels is discussed. Experimental investigations reveal that seepage, either in the downward direction (suction) or in the upward direction (injection), can significantly change the resistance as well as the mobility of the sand-bed particles. A resistance equation relating 'particle Reynolds number' and 'shear Reynolds number' under seepage conditions is developed for plane sediment beds. Finally, a detailed design procedure of the plane sediment beds affected by seepage is presented.

OCR Prediction Using Support Vector Machine Based on Piezocone Data

The determination of the overconsolidation ratio (OCR) of clay deposits is an important task in geotechnical engineering practice. This paper examines the potential of a support vector machine (SVM) for predicting the OCR of clays from piezocone penetration test data. SVM is a statistical learning theory based on a structural risk minimization principle that minimizes both error and weight terms. The five input variables used for the SVM model for prediction of OCR are the corrected cone resistance (qt), vertical total stress (sigmav), hydrostatic pore pressure (u0), pore pressure at the cone tip (u1), and the pore pressure just above the cone base (u2). Sensitivity analysis has been performed to investigate the relative importance of each of the input parameters. From the sensitivity analysis, it is clear that qt=primary in situ data influenced by OCR followed by sigmav, u0, u2, and u1. Comparison between SVM and some of the traditional interpretation methods is also presented. The results of this study have shown that the SVM approach has the potential to be a practical tool for determination of OCR.

Uplink Power Control and Base Station Association in Multichannel Cellular Networks

A combined base station association and power control problem is studied for the uplink of multichannel multicell cellular networks, in which each channel is used by exactly one cell (i.e., base station). A distributed association and power update algorithm is proposed and shown to converge to a Nash equilibrium of a noncooperative game. We consider network models with discrete mobiles (yielding an atomic congestion game), as well as a continuum of mobiles (yielding a population game). We find that the equilibria need not be Pareto efficient, nor need they be system optimal. To address the lack of system optimality, we propose pricing mechanisms. It is shown that these mechanisms can be implemented in a distributed fashion.

Resource recovery potential from secondary components of segregated municipal solid wastes

Fermentable components of municipal solid wastes (MSW) such as fruit and vegetable wastes (FVW), leaf litter, paddy straw, cane bagasse, cane trash and paper are generated in large quantities at various pockets of the city. These form potential feedstocks for decentralized biogas plants to be operated in the vicinity. We characterized the fermentation potential of six of the above MSW fractions for their suitability to be converted to biogas and anaerobic compost using the solid-state stratified bed (SSB) process in a laboratory study. FVW and leaf litter (papermulberry leaves) decomposed almost completely while paddy straw, sugarcane trash, sugarcane bagasse and photocopying paper decomposed to a lower extent. In the SSB process between 50-60% of the biological methane potential (BMP) could be realized. Observations revealed that the SSB process needs to be adapted differently for each of the feedstocks to obtain a higher gas recovery. Bagasse produced the largest fraction of anaerobic compost (fermentation residue) and has the potential for reuse in many ways.

Robust heuristics for scalable optimization of complex SQL queries

Modern database systems incorporate a query optimizer to identify the most efficient "query execution plan" for executing the declarative SQL queries submitted by users. A dynamic-programming-based approach is used to exhaustively enumerate the combinatorially large search space of plan alternatives and, using a cost model, to identify the optimal choice. While dynamic programming (DP) works very well for moderately complex queries with up to around a dozen base relations, it usually fails to scale beyond this stage due to its inherent exponential space and time complexity. Therefore, DP becomes practically infeasible for complex queries with a large number of base relations, such as those found in current decision-support and enterprise management applications. To address the above problem, a variety of approaches have been proposed in the literature. Some completely jettison the DP approach and resort to alternative techniques such as randomized algorithms, whereas others have retained DP by using heuristics to prune the search space to computationally manageable levels. In the latter class, a well-known strategy is "iterative dynamic programming" (IDP) wherein DP is employed bottom-up until it hits its feasibility limit, and then iteratively restarted with a significantly reduced subset of the execution plans currently under consideration. The experimental evaluation of IDP indicated that by appropriate choice of algorithmic parameters, it was possible to almost always obtain "good" (within a factor of twice of the optimal) plans, and in the few remaining cases, mostly "acceptable" (within an order of magnitude of the optimal) plans, and rarely, a "bad" plan. While IDP is certainly an innovative and powerful approach, we have found that there are a variety of common query frameworks wherein it can fail to consistently produce good plans, let alone the optimal choice. This is especially so when star or clique components are present, increasing the complexity of th- e join graphs. Worse, this shortcoming is exacerbated when the number of relations participating in the query is scaled upwards.

The syntheses, characterizations, X-ray crystal structures and properties of Cu(I) complexes of a bis-bidentate schiff base ligand

Bis-bidentate Schiff base ligand L and its two mononuclear complexes [CuL(CH3CN)(2)]ClO4 (1)and [CuL(PPh3)(2)]ClO4 (2)have been prepared and thoroughly characterized by elemental analyses, IR, UV-Vis, NMR spectroscopy and X-ray diffraction analysis. In both the complexes the metal ion auxiliaries adopt tetrahedral coordination environment. Their reactivity, electrochemical and photophysical behavior have been studied. Complex 1 shows reversible Cu-II/I couple with potential 0.74 V versus Ag/AgCl in CH2Cl2. At room temperature L is weakly fluorescent in CH2Cl2, however in Cu(I)complexes 1 and 2 the emission in quenched. (C) 2009 Elsevier B. V. All rights reserved.

Study of gas cavity size hysteresis in a packed bed using DEM

When a high velocity gas jet is introduced into a packed bed a cavity is formed. The size of the cavity shows hysteresis on increasing and decreasing gas flow rates. This hysteresis leads to different cavity sizes at same gas flow rate depending on the bed history. The size of cavity affects the gas flow profiles in the packed bed. In this study the cavity size hysteresis phenomenon has been modeled using discrete element method along with turbulent gas flow. A reasonable agreement has been found between computed and experimental results on cavity size ysteresis. The effect of various parameters, such as nozzle height from the bed bottom and packing height, on the cavity size hysteresis has been studied. It is found that inter-particle interaction forces along with gas drag and bed porosity play an important role in describing the cavity size hysteresis. The injection of gas flow allows the particles to go to an unconstrained state than they were previously in, and their ability to remain in that state, even under decreased gas drag force, leads to the phenomenon of cavity size hysteresis. (c) 2007 Elsevier Ltd. All rights reserved.

A generalized mathematical theory and experimental verification of proportional notches

A theory and generalized synthesis procedure is advocated for the design of weir notches and orifice-notches having a base in any given shape, to a depth a, such that the discharge through it is proportional to any singular monotonically-increasing function of the depth of flow measured above a certain datum. The problem is reduced to finding an exact solution of a Volterra integral equation in Abel form. The maximization of the depth of the datum below the crest of the notch is investigated. Proof is given that for a weir notch made out of one continuous curve, and for a flow proportional to the mth power of the head, it is impossible to bring the datum lower than (2m − 1)a below the crest of the notch. A new concept of an orifice-notch, having discontinuity in the curve and a division of flow into two distinct portions, is presented. The division of flow is shown to have a beneficial effect in reducing the datum below (2m − 1)a from the crest of the weir and still maintaining the proportionality of the flow. Experimental proof with one such orifice-notch is found to have a constant coefficient of discharge of 0.625. The importance of this analysis in the design of grit chambers is emphasized.