Functional correlation of bacterial LuxS with their quaternary associations: interface analysis of the structure networks

Background The genome of a wide variety of prokaryotes contains the luxS gene homologue, which encodes for the protein S-ribosylhomocysteinelyase (LuxS). This protein is responsible for the production of the quorum sensing molecule, AI-2 and has been implicated in a variety of functions such as flagellar motility, metabolic regulation, toxin production and even in pathogenicity. A high structural similarity is present in the LuxS structures determined from a few species. In this study, we have modelled the structures from several other species and have investigated their dimer interfaces. We have attempted to correlate the interface features of LuxS with the phenotypic nature of the organisms. Results The protein structure networks (PSN) are constructed and graph theoretical analysis is performed on the structures obtained from X-ray crystallography and on the modelled ones. The interfaces, which are known to contain the active site, are characterized from the PSNs of these homodimeric proteins. The key features presented by the protein interfaces are investigated for the classification of the proteins in relation to their function. From our analysis, structural interface motifs are identified for each class in our dataset, which showed distinctly different pattern at the interface of LuxS for the probiotics and some extremophiles. Our analysis also reveals potential sites of mutation and geometric patterns at the interface that was not evident from conventional sequence alignment studies. Conclusion The structure network approach employed in this study for the analysis of dimeric interfaces in LuxS has brought out certain structural details at the side-chain interaction level, which were elusive from the conventional structure comparison methods. The results from this study provide a better understanding of the relation between the luxS gene and its functional role in the prokaryotes. This study also makes it possible to explore the potential direction towards the design of inhibitors of LuxS and thus towards a wide range of antimicrobials.

In search of inorganic nonlinear optical materials for second harmonic generation

In a search for inorganic oxide materials showing second-order nonlinear optical (NLO) susceptibility, we investigated several berates, silicates, and a phosphate containing trans-connected MO6, octahedral chains or MO5 square pyramids, where, M = d(0): Ti(IV), Nb(V), or Ta(V), Our investigations identified two new NLO structures: batisite, Na2Ba(TiO)(2)Si4O12, containing trans-connected TiO5 octahedral chains, and fresnoite, Ba2TiOSi2O7, containing square-pyramidal TiO5. Investigation of two other materials containing square-pyramidal TiO5 viz,, Cs2TiOP2O7 and Na4Ti2Si8O22. 4H(2)O, revealed that isolated TiO5, square pyramids alone do not cause a second harmonic generation (SHG) response; rather, the orientation of TiO5 units to produce -Ti-O-Ti-O- chains with alternating long and short Ti-O distances in the fresnoite structure is most likely the origin of a strong SHG response in fresnoite,

Energy-momentum conserving algorithm for nonlinear transient analysis within the framework of hybrid elements

This work deals with the formulation and implementation of an energy-momentum conserving algorithm for conducting the nonlinear transient analysis of structures, within the framework of stress-based hybrid elements. Hybrid elements, which are based on a two-field variational formulation, are much less susceptible to locking than conventional displacement-based elements within the static framework. We show that this advantage carries over to the transient case, so that not only are the solutions obtained more accurate, but they are obtained in fewer iterations. We demonstrate the efficacy of the algorithm on a wide range of problems such as ones involving dynamic buckling, complicated three-dimensional motions, et cetera.

Trehalose Toxicity in Cuscuta refexal Correlation With low Trehalase Activity

A toxic effect of a,a-trehalose in an angiospermic plant, Cuscuta reflexa (dodder), Is described. This disaccharide and Its analogs, 2-aminotrehalose and 4-aminotbhakose, induced a raid blackening of the terminal region of the vine which is Involved in elongation growth. From the results of in vitro growth of several angkiopermic plants and determination of trehalase activity in them, it is concluded that the toxic effect of trehalose in Cucaa is because of the very low trehalas activity In the vine. As a result, trehalose accumulates In the vine and interferes with some process closely associated with growth. The growth potential of Lemma (a duckweed) in a medium containing trehalose as the carbon source was ihreversibly lost upon addition of trealosamine, an Inhibitor of trehalase activity. It is concluded that, if allowed to accumulate within the tissue, trehalose may be potentiaMly toxic or inhibitory to higher plants in generaL The presence of trhalase actvity in plants, where Its substrate has not been found to occur, is envisged to relieve the plant from the toxic effects of trehalose which it may encounter in soil or during association with fungi or insects.

Mesh-free approximations via the error reproducing kernel method and applications to nonlinear systems developing shocks

Error estimates for the error reproducing kernel method (ERKM) are provided. The ERKM is a mesh-free functional approximation scheme [A. Shaw, D. Roy, A NURBS-based error reproducing kernel method with applications in solid mechanics, Computational Mechanics (2006), to appear (available online)], wherein a targeted function and its derivatives are first approximated via non-uniform rational B-splines (NURBS) basis function. Errors in the NURBS approximation are then reproduced via a family of non-NURBS basis functions, constructed using a polynomial reproduction condition, and added to the NURBS approximation of the function obtained in the first step. In addition to the derivation of error estimates, convergence studies are undertaken for a couple of test boundary value problems with known exact solutions. The ERKM is next applied to a one-dimensional Burgers equation where, time evolution leads to a breakdown of the continuous solution and the appearance of a shock. Many available mesh-free schemes appear to be unable to capture this shock without numerical instability. However, given that any desired order of continuity is achievable through NURBS approximations, the ERKM can even accurately approximate functions with discontinuous derivatives. Moreover, due to the variation diminishing property of NURBS, it has advantages in representing sharp changes in gradients. This paper is focused on demonstrating this ability of ERKM via some numerical examples. Comparisons of some of the results with those via the standard form of the reproducing kernel particle method (RKPM) demonstrate the relative numerical advantages and accuracy of the ERKM.

Studies in Nonlinear Optical Materials: Structure of 3-Menthyl 2-[Bis(dimethylarnino)methylene]-3-oxobutyrate Hemihydrate

C 19Ha4N203.~xH 2 O, Mr= 347.5, monoclinic, C2, a = 15.473 (3), b = 6.963 (2), c = 20.708 (4) ]1, //=108.2(2) ° , V=2119(2)A 3, Z=4, Ox= 1.089 Mg m -3, ,~(Cu Ktx) = 1.5418 ]1, p = 0.523 mm -~, F(000) = 760.0, T= 293 K, R = 0.068 for 1967 unique reflections. The C=C bond length is 1-447 (6)]1, significantly longer than in ethylene, 1.336 (2)]1. The crystal structure is stabilized by O-H...O hydrogen bonding. Explanation for the observed low second-harmonic-generation efficiency (0.5 times that of urea) is provided.

Structure-reactivity correlation in inclusion complexes: deoxycholic acid di-tert-butyl thioketone

Ultraviolet irradiation of crystalline molecular inclusion complexes of deoxycholic acid with di-tert-butyl thioketone results in no reaction. The structure of the above complex has been determined via X-ray diffraction. The absence of expected photoreactions. namely, photoreduction and photooxidation, is rationalized on the basis of the X-ray structure analysis of the complex.

Studies in Nonlinear Optical Materials: Structure of Methyl 2-(4-Ethyl-5-methyl- 2-thioxo-2,3-dihydro-l,3-thiazol- 3-yl) propionate

CIoH15NO282, Mr=245"0, orthorhombic, P21212 ~, a = 6.639 (2), b = 8.205 (2), c = 22.528(6)A, V= I227.2(6)A 3, z=4, Dm= 1.315, Dx= 1.326gem -3, MoKa, 2=0.7107A, 12= 3.63 cm -1, F(000) = 520, T= 293 K, R = 0.037 for 1115 significant reflections. The second-harmonicgeneration (SHG) efficiency of this compound is only 1/10th of the urea standard. The observed low second-order nonlinear response may be attributed to the unfavourable packing of the molecules in the crystal lattice.

A Nonlinear System Under Combined Periodic and Random Excitation

The anharmonic oscillator under combined sinusoidal and white noise excitation is studied using the Gaussian closure approximation. The mean response and the steady-state variance of the system is obtained by the WKBJ approximation and also by the Fokker Planck equation. The multiple steadystate solutions are obtained and their stability analysis is presented. Numerical results are obtained for a particular set of system parameters. The theoretical results are compared with a digital simulation study to bring out the usefulness of the present approximate theory.

Nonlinear I-V characteristics of senmiconducting paints

The oxide-based high resistivity semiconducting Paints can be used on high voltage insulators for improved performance. They were found to exhibit nonlinear I-V characteristics which are reported here. The paints exhibited power law relationship and a sharp transition in merhanism of conduction at a critical voltage.

3-D kinematical conservation laws (KCL): Evolution of a surface in R-3 - in particular propagation of a nonlinear wavefront

3-D KCL are equations of evolution of a propagating surface (or a wavefront) Omega(t), in 3-space dimensions and were first derived by Giles, Prasad and Ravindran in 1995 assuming the motion of the surface to be isotropic. Here we discuss various properties of these 3-D KCL.These are the most general equations in conservation form, governing the evolution of Omega(t) with singularities which we call kinks and which are curves across which the normal n to Omega(t) and amplitude won Omega(t) are discontinuous. From KCL we derive a system of six differential equations and show that the KCL system is equivalent to the ray equations of 2, The six independent equations and an energy transport equation (for small amplitude waves in a polytropic gas) involving an amplitude w (which is related to the normal velocity m of Omega(t)) form a completely determined system of seven equations. We have determined eigenvalues of the system by a very novel method and find that the system has two distinct nonzero eigenvalues and five zero eigenvalues and the dimension of the eigenspace associated with the multiple eigenvalue 0 is only 4. For an appropriately defined m, the two nonzero eigenvalues are real when m > 1 and pure imaginary when m < 1. Finally we give some examples of evolution of weakly nonlinear wavefronts.

Pulsed laser surface treatment of magnesium alloy: Correlation between thermal model and experimental observations

The effect of deposition of Al +Al2O3 on MRI 153 M Mg alloy processed using a pulsed Nd:YAG laser is presented in this study. A composite coating with metallurgical joint to the substrate was formed. The microstructure and phase constituents were characterized and correlated with the thermal predictions. The laser scan speed had an effect on the average melt depth and the amount of retained and/or reconstituted alumina in the final coating. The coating consisted of alumina particles and highly refined dendrites formed due to the extremely high cooling rates (of the order of 10(8) K/s). The microhardness of the coating was higher and several fold improvement of wear resistance compared to the substrate was observed for the coatings. These microstructural features and physical properties were correlated with the effects predicted by a thermal model.

Nonlinear transport in semiconducting polymers at high carrier densities

Conducting and semiconducting polymers are important materials in the development of printed, flexible, large-area electronics such as flat-panel displays and photovoltaic cells. There has been rapid progress in developing conjugated polymers with high transport mobility required for high-performance field-effect transistors (FETs), beginning(1) with mobilities around 10(-4) cm(2) V-1 s(-1) to a recent report(2) of 1 cm(2) V-1 s(-1) for poly(2,5-bis(3-tetradecylthiophen-2-yl) thieno[3,2-b] thiophene) (PBTTT). Here, the electrical properties of PBTTT are studied at high charge densities both as the semiconductor layer in FETs and in electrochemically doped films to determine the transport mechanism. We show that data obtained using a wide range of parameters (temperature, gate-induced carrier density, source-drain voltage and doping level) scale onto the universal curve predicted for transport in the Luttinger liquid description of the one-dimensional `metal'.

Correlation Between The Stability Of Carbonates In Ternary Ln2o3-H2o-Co2 Hydrothermal Systems And Lanthanide Systematics

Phase diagrams for ternary Ln2O3-H2O-CO2 systems for the entire lanthanide series (except promethium) were studied at temperatures in the range 100–950 °C and pressures up to 3000 bar. The phase diagrams obtained for the heavier lanthanides are far more complex, with the appearance of a number of stable carbonate phases. New carbonates isolated from lanthanide systems (Ln ≡ Tm, Yb, Lu) include Ln6(OH)4(CO3)7, Ln4(OH)6-(CO3)3, Ln2O(OH)2CO3, Ln6O2(OH)8(CO3)3 and Ln12O7(OH)10(CO3)6. Stable carbonate phases common to all the lighter lanthanides are hexagonal LnOHCO3 and hexagonal Ln2O2CO3. Ln2(CO3)3• 3H2O is stable from samarium onwards and orthorhombic LnOHCO3 is stable from gadolinium onwards. On the basis of the appearance of stable carbonates, four different groups of lanthanides were established: lanthanum to neodymium, promethium to europium, terbium to erbium and thulium to lutetium. Gadolinium is the connecting element between groups II and III. This is in accordance with the tetrad classification for f transition elements.

Nonlinear conduction and electrical switching in one-dimensional conductors

Many one-dimensional conductors show pronounced nonlinear electrical conduction. Some of them show very interesting electrical switching from a low conducting state to a high conducting state. Such electrical switching is often associated with memory. These are discussed with particular emphasis on charge transfer complexestmbine-tcnq, tmpd-tcnq, Cs2(tcnq)3,tea-(tcnq) 2 ando-tolidine-iodine.