A nanosecond molecular dynamics study of antiparallel d(G)(7) quadruplex structures: Effect of the coordinated cations

Nanosecond scale molecular dynamics simulations have been performed on antiparallel Greek key type d(G(7)) quadruplex structures with different coordinated ions, namely Na+ and K+ ion, water and Na+ counter ions, using the AMBER force field and Particle Mesh Ewald technique for electrostatic interactions. Antiparallel structures are stable during the simulation, with root mean square deviation values of similar to1.5 Angstrom from the initial structures. Hydrogen bonding patterns within the G-tetrads depend on the nature of the coordinated ion, with the G-tetrad undergoing local structural variation to accommodate different cations. However, alternating syn-anti arrangement of bases along a chain as well as in a quartet is maintained through out the MD simulation. Coordinated Na+ ions, within the quadruplex cavity are quite mobile within the central channel and can even enter or exit from the quadruplex core, whereas coordinated K+ ions are quite immobile. MD studies at 400 K indicate that K+ ion cannot come out from the quadruplex core without breaking the terminal G-tetrads. Smaller grooves in antiparallel structures are better binding sites for hydrated counter ions, while a string of hydrogen bonded water molecules are observed within both the small and large grooves. The hydration free energy for the K+ ion coordinated structure is more favourable than that for the Na+ ion coordinated antiparallel quadruplex structure.

Real-time multipurpose reservoir operation: a case study / Exploitation en temps reacuteel d'un reservoir agrave buts multiples: eacutetude d'un cas

A real-time operational methodology has been developed for multipurpose reservoir operation for irrigation and hydropower generation with application to the Bhadra reservoir system in the state of Karnataka, India. The methodology consists of three phases of computer modelling. In the first phase, the optimal release policy for a given initial storage and inflow is determined using a stochastic dynamic programming (SDP) model. Streamflow forecasting using an adaptive AutoRegressive Integrated Moving Average (ARIMA) model constitutes the second phase. A real-time simulation model is developed in the third phase using the forecast inflows of phase 2 and the operating policy of phase 1. A comparison of the optimal monthly real-time operation with the historical operation demonstrates the relevance, applicability and the relative advantage of the proposed methodology.

Effect of substrate temperature on the properties of ZrO2 films prepared by d.c. reactive magnetron sputtering

Studies of ZrO2 films prepared by d.c. reactive magnetron sputtering are described. The effects of substrate temperature on the packing density, refractive index, extinction coefficient and crystallinity phase have been investigated in the temperature range 25–450 °C. The refractive index varied from 1.84 to 1.95 and extinction coefficient from 2 × 10−3 to 9.6 × 10−3. This was explained on the basis of an increase in packing density from 0.686 to 0.813. The change in packing density has been attributed to a decrease in the oxygen condensation at higher temperatures. Annealing results in a decrease in refractive index and increase in extinction coefficient. The films deposited at 150 °C showed a monoclinic phase which transforms to a tetragonal phase at higher substrate temperatures.

Structural Polymorphism in d(T).d(A)*d(T) Triple Helices

DNA triple helices containing two thymine strands and one adenine strand have been studied, using model building followed by energy minimisation, for different orientations of the third strand resulting from variation in the hydrogen bonding between the Watson-Crick duplex and the third strand and the glycosidic torsion angle in the third strand. Our results show that the structure with a parallel orientation of the third strand, in which the third strand base forms Hoogsteen hydrogen bonds with the adenine base in the Watson-Crick duplex, is energetically the most favourable. An antiparallel orientation of the third strand is also possible, in which the third strand base hydrogen bonds to both the bases in the Watson-Crick duplex. This structure is energetically comparable to the parallel structure. For the parallel triplex a 200ps molecular dynamics simulation starting from two different starting structures indicates that at 300K significant structural heterogeneity exists in this tripler structure. The results are compared with existing structural data on this class of triplexes derived from theoretical and NMR techniques.

Conformational Polymorphism in Telomeric Structures: Loop Orientation and Interloop Pairing in d(G4TnG4),

Sequence repeats constituting the telomeric regions of chromosomes are known to adopt a variety of unusual structures, consisting of a G tetraplex stem and short stretches of thymines or thymines and adenines forming loops over the stem. Detailed model building and molecular mechanics studies have been carried out for these telomeric sequences to elucidate different types of loop orientations and possible conformations of thymines in the loop. The model building studies indicate that a minimum of two thymines have to be interspersed between guanine stretches to form folded-back structures with loops across adjacent strands in a G tetraplex (both over the small as well as large groove), while the minimum number of thymines required to build a loop across the diagonal strands in a G tetraplex is three. For two repeat sequences, these hairpins, resulting from different types of folding, can dimerize in three distinct ways-i.e., with loops across adjacent strands and on same side, with loops across adjacent strands and on opposite sides, and with loops across diagonal strands and on opposite sides-to form hairpin dimer structures. Energy minimization studies indicate that all possible hairpin dimers have very similar total energy values, though different structures are stabilized by different types of interactions. When the two loops are on the same side, in the hairpin dimer structures of d(G(4)T(n)G(4)), the thymines form favorably stacked tetrads in the loop region and there is interloop hydrogen bonding involving two hydrogen bonds for each thymine-thymine pair. Our molecular mechanics calculations on various folded-back as well as parallel tetraplex structures of these telomeric sequences provide a theoretical rationale for the experimentally observed feature that the presence of intervening thymine stretches stabilizes folded-back structures, while isolated stretches of guanines adopt a parallel tetraplex structure

Activation barriers for d.c. conductivity in ionic glasses: Classical calculations using the small-cluster approximation

A small-cluster approximation has been used to calculate the activation barriers for the d.c. conductivity in ionic glasses. The main emphasis of this approach is on the importance of the hitherto ignored polarization energy contribution to the total activation energy. For the first time it has been demonstrated that the d.c. conductivity activation energy can be calculated by considering ionic migration to a neighbouring vacancy in a smali cluster of ions consisting of face-sharing anion polyhedra. The activation energies from the model calculations have been compared with the experimental values in the case of highly modified lithium thioborate glasses.

Purification of 3,5-Dichlorocatechol 1,2-Dioxygenase, a Nonheme Iron Dioxygenase and a Key Enzyme in the Biodegradation of a Herbicide, 2,4-Dichlorophenoxyacetic acid (2,4-D), from Pseudomonas cepacia CSV90

An enzyme which cleaves the benzene ring of 3,5-dichiorocatechol has been purified to homogeneity from Pseudomonas cepacia CSV90, grown with 2,4-dichlorophenoxyacetic acid (2,4-D) as the sole carbon source. The enzyme was a nonheme ferric dioxygenase and catalyzed the intradiol cleavage of all the examined catechol derivatives, 3,5-dichlorocatechol having the highest specificity constant of 7.3 μM−1 s−1 in an air-saturated buffer. No extradiol-cleaving activity was observed. Thus, the enzyme was designated as 3,5-dichlorocatechol 1,2-dioxygenase. The molecular weight of the native enzyme was ascertained to be 56,000 by light scattering method, while the Mr value of the enzyme denatured with 6 M guanidine-HCl or sodium dodecyl sulfate was 29,000 or 31,600, respectively, suggesting that the enzyme was a homodimer. The iron content was estimated to be 0.89 mol per mole of enzyme. The enzyme was deep red and exhibited a broad absorption spectrum with a maximum at around 425 nm, which was bleached by sodium dithionite, and shifted to 515 nm upon anaerobic 3,5-dichlorocatechol binding. The catalytic constant and the Km values for 3,5-dichlorocatechol and oxygen were 34.7 s−1 and 4.4 and 652 μM, respectively, at pH 8 and 25°C. Some heavy metal ions, chelating agents and sulfhydryl reagents inhibited the activity. The NH2-terminal sequence was determined up to 44 amino acid residues and compared with those of the other catechol dioxygenases previously reported.

Synthesis of Layered Perovskite Oxides, ACa2-xLaxNb3-xTix010 (A = K, Rb, Cs), and Characterization of New Solid Acids, HCa2-xLaxNb3-xTixOlo (0 < x d 2), Exhibiting Variable Bronsted Acidity?

Layered perovskite oxides of the formula ACa~,La,Nb3-,Ti,010 (A = K, Rb, Cs and 0 < x d 2) have been prepared. The members adopt the structures of the parent ACazNb3010. Interlayer alkali cations in the niobium-titanium oxide series can be ion-exchanged with Li+, Na+, NH4+, or H+ to give new derivatives. Intercalation of the protonated derivatives with organic bases reveals that the Bronsted acidity of the solid solution series, HC~ ~ , L ~ ,N~ ~ , T ~ ,dOep~eOnd, s on the titanium content. While the x = 1 member (HCaLaNbzTiOlo) is nearly as acidic as the parent HCazNb3010, the x = 2 member (HLazNbTizOlo) is a weak acid hardly intercalating organic bases with pKa - 11.3. The variation of acidity is probably due to an ordering of Nb/Ti atoms in the triple octahedral perovskite slabs, [Ca~,La,Nb~,Ti,0~0], such that protons are attached to NbO6 octahedra in the x = 1 member and to Ti06 octahedra in the x = 2 member.

Effective action and adiabatic expansions for the 1-D and 2-D hubbard models at half-filling

We analyze here the occurrence of antiferromagnetic (AFM) correlations in the half-filled Hubbard model in one and two space dimensions using a natural fermionic representation of the model and a newly proposed way of implementing the half-filling constraint. We find that our way of implementing the constraint is capable of enforcing it exactly already at the lowest levels of approximation. We discuss how to develop a systematic adiabatic expansion for the model and how Berry's phase contributions arise quite naturally from the adiabatic expansion. At low temperatures and in the continuum limit the model gets mapped onto an O(3) nonlinear sigma model (NLsigma). A topological, Wess-Zumino term is present in the effective action of the ID NLsigma as expected, while no topological terms are present in 2D. Some specific difficulties that arise in connection with the implementation of an adiabatic expansion scheme within a thermodynamic context are also discussed, and we hint at possible solutions.

Modified Crack Closure Integral (MCCI) For 3-D Problems Using 20-Noded Brick Elements

The Modified Crack Closure Integral (MCCI) technique based on Irwin's crack closure integral concept is very effective for estimation of strain energy release rates G in individual as well as mixed-mode configurations in linear elastic fracture mechanics problems. In a finite element approach, MCCI can be evaluated in the post-processing stage in terms of nodal forces and displacements near the crack tip. The MCCI expressions are however, element dependent and require a systematic derivation using stress and displacement distributions in the crack tip elements. Earlier a general procedure was proposed by the present authors for the derivation of MCCI expressions for 3-dimensional (3-d) crack problems modelled with 8-noded brick elements. A concept of sub-area integration was proposed to estimate strain energy release rates at a large number of points along the crack front. In the present paper a similar procedure is adopted for the derivation of MCCI expressions for 3-d cracks modelled with 20-noded brick elements. Numerical results are presented for centre crack tension and edge crack shear specimens in thick slabs, showing a comparison between present results and those available in the literature.

Hydrogen-bond-directed self-assembly of D-(+)-dibenzoyltartaric acid and 4-aminopyridine: optical nonlinearities and stoichiometry-dependent novel structural features

Attempts to prepare hydrogen-bond-directed nonlinear optical materials from a 1:1 molar mixture Of D-(+)-dibenzoyltartaric acid (DBT, I) and 4-aminopyridine (4-AP, II) resulted in two salts of different stoichiometry. One of them crystallizes in an unusual 1.5:1 (acid:base) monohydrate salt form III while the other one crystallizes as 1:1 (acid:base) salt IV. Crystal structures of both of the salts were determined from single-crystal X-ray diffraction data. The salt III crystallizes in a monoclinic space group C2 with a = 30.339(l), b = 7.881(2), c = 14.355(1) angstrom, beta = 97.48(1)degrees, V = 3403.1(9) angstrom3, Z = 4, R(w) = 0.058, R(w)= 0.058. The salt IV also crystallizes in a monoclinic space group P2(1) with a = 7.500(1), b = 14.968(2), c = 10.370(1) angstrom, beta = 102.67(1)degrees, V = 1135.9(2) angstrom3, Z = 2, R = 0.043, R(w) = 0.043. Interestingly, two DBT molecules with distinctly different conformation are present in the same crystal lattice of salt III. Extensive hydrogen-bonding interactions are found in both of the salts, and both of them show SHG intensity 1.4-1.6 times that of urea.

Modified crack closure integral (MCCI) for 3-d problems using 20 noded brick elememnts

The Modified Crack Closure Integral (MCCI) technique based on Irwin's crack closure integral concept is very effective for estimation of strain energy release rates G in individual as well as mixed-mode configurations in linear elastic fracture mechanics problems. In a finite element approach, MCCI can be evaluated in the post-processing stage in terms of nodal forces and displacements near the crack tip. The MCCI expressions are however, element dependent and require a systematic derivation using stress and displacement distributions in the crack tip elements. Earlier a general procedure was proposed by the present authors for the derivation of MCCI expressions for 3-dimensional (3-d) crack problems modelled with 8-noded brick elements. A concept of sub-area integration was proposed to estimate strain energy release rates at a large number of points along the crack front. In the present paper a similar procedure is adopted for the derivation of MCCI expressions for 3-d cracks modelled with 20-noded brick elements. Numerical results are presented for centre crack tension and edge crack shear specimens in thick slabs, showing a comparison between present results and those available in the literature.

Proportioning of fly-ash cement concrete mixes

The accumulation of fly ash throughout the world is several million tons per day. The main problem with the usage of fly ash is the slow rate of strength gain, primarily due to slow pozzolanic reactions. Existing methods of proportioning fly ash concrete are lacking. These methods are involved and do not directly take into account the properties of the constituent materials. The Generalized Approach for Mix Proportioning developed at the Indian Institute of Science, Bangalore, is the basis for the development of the proposed method, which takes into account the characteristics of cement, fly ash, and aggregates. Based on the basic trial mix data obtained by using the American Concrete Institute (ACI 211.1-81) method, the proportions of fly-ash concrete mixes were arrived at using the Generalized Approach for Mix Proportioning. The method proposed was applied to and found applicable for fly-ash concretes using fly ashes from two different sources.

Structural Behavior of Story-High Cement-Stabilized Rammed-Earth Walls under Compression

A rammed-earth wall is a monolithic construction made by compacting processed soil in progressive layers in a rigid formwork. There is a growing interest in using this low-embodied-carbon building material in buildings. The paper investigates the strength and structural behavior of story-high cement-stabilized rammed-earth (CSRE) walls, reviews literature on the strength of CSRE, and discusses results of the compressive strength of CSRE prisms, wallettes, and story-high walls. The strength of the story-high wall was compared with the strength of wallettes and prisms. There is a nearly 30% reduction in strength as the height-to-thickness ratio increases from about 5 to 20. The ultimate compressive strength of CSRE walls predicted using the tangent modulus theory is in close agreement with the experimental values. The shear failures noticed in the story-high walls resemble the shear failures of short-height prism and wallette specimens. The paper ends with a discussion of structural design and characteristic compressive strength of CSRE walls. DOI: 10.1061/(ASCE)MT.1943-5533.0000155. (C) 2011 American Society of Civil Engineers.