Identification of Local Conformational Similarity in Structurally Variable Regions of Homologous Proteins Using Protein Blocks

Structure comparison tools can be used to align related protein structures to identify structurally conserved and variable regions and to infer functional and evolutionary relationships. While the conserved regions often superimpose well, the variable regions appear non superimposable. Differences in homologous protein structures are thought to be due to evolutionary plasticity to accommodate diverged sequences during evolution. One of the kinds of differences between 3-D structures of homologous proteins is rigid body displacement. A glaring example is not well superimposed equivalent regions of homologous proteins corresponding to a-helical conformation with different spatial orientations. In a rigid body superimposition, these regions would appear variable although they may contain local similarity. Also, due to high spatial deviation in the variable region, one-to-one correspondence at the residue level cannot be determined accurately. Another kind of difference is conformational variability and the most common example is topologically equivalent loops of two homologues but with different conformations. In the current study, we present a refined view of the ``structurally variable'' regions which may contain local similarity obscured in global alignment of homologous protein structures. As structural alphabet is able to describe local structures of proteins precisely through Protein Blocks approach, conformational similarity has been identified in a substantial number of `variable' regions in a large data set of protein structural alignments; optimal residue-residue equivalences could be achieved on the basis of Protein Blocks which led to improved local alignments. Also, through an example, we have demonstrated how the additional information on local backbone structures through protein blocks can aid in comparative modeling of a loop region. In addition, understanding on sequence-structure relationships can be enhanced through our approach. This has been illustrated through examples where the equivalent regions in homologous protein structures share sequence similarity to varied extent but do not preserve local structure.

Positional Consensus of Multi-Agent Systems Using Linear Programming Based Decentralized Control with Rectilinear Decision Domain

In this paper we develop a Linear Programming (LP) based decentralized algorithm for a group of multiple autonomous agents to achieve positional consensus. Each agent is capable of exchanging information about its position and orientation with other agents within their sensing region. The method is computationally feasible and easy to implement. Analytical results are presented. The effectiveness of the approach is illustrated with simulation results.

Linear electro‐optic dispersion in (‐)‐2‐(α‐methylbenzylamino)‐5‐nitropyridine single crystals

The variation of the linear electro-optic effect in (-)-2-(alpha-methylbenzylamino)-5-nitropyridine with the wavelength of the incident light at room temperature has been measured. The reduced half-wave voltages have been found to have the values 2.1, 2.8, and 6.0 kV at 488, 514.5, and 632.8 nm respectively and the corresponding values of the linear electro-optic coefficient have been evaluated.;The interpretation of the results in terms of the structures of the molecule and the crystal is discussed. The thermal variation of the birefringence has also been investigated and the coefficient for the temperature variation of the refractive index difference is found to have the value (d Delta n/dT)=9.3X10(-5) K-1.

Non-Linear effects of membrane fluctuations in the dilute lamellar phase

The static structure factor of the dilute sterically stabilised lamellar phase is calculated and found to have an Ornstein-Zernike form with a correlation length that diverges at infinite dilution. The relaxation time for concentration fluctuations at large wave number q is shown to go as q-3 with a coefficient independent of the membrane bending rigidity. The membrane fluctuations also give rise to strongly frequency-dependent viscosities at high frequencies.

Practical constant-accuracy linear weir

This paper is concerned with the modifications of the Extended Bellmouth Weir (EBM weir) earlier designed by Keshava Murthy. It is shown that by providing inclined sides (equivalent to providing an inward-trapezoidal weir) over a sector of a circle of radius R, separated by a distance 2t, and depth d, the measurable range of EBM can be considerably enhanced (over 375%). Simultaneously, the other parameters of the weir are optimized such that the reference plane of the weir coincides with its crest making it a constant-accuracy linear weir. Discharge through the aforementioned weir is proportional to the depths of flow measured above the crest of the weir for all heads in the range of 0.5R less-than-or-equal-to h less-than-or-equal-to 7.9R, within a maximum deviation of +/-1% from the theoretical discharge. Experiments with two typical weirs show excellent agreement with the theory by giving a constant-average coefficient of discharge of 0.619

Linear optical properties of BaNaB9O15, BaLiB9O15 and SrLiB9O15 glasses

Transparent BaNaB9O15 (BNBO), BaLiB9O15 (BLBO) and SrLiB9O15 (SLBO) glasses were fabricated via the conventional melt-quenching technique. X-ray diffraction (XRD) and Differential thermal analysis (DTA) studies carried out on the as-quenched glasses confirmed their amorphous and glassy nature, respectively. The optical properties for these as-quenched glasses were investigated. The refractive index, optical band gap. Urbach energy and Fermi energy were determined. The average electronic polarizability calculated from the refractive index expression. (C) 2011 Elsevier B.V. All rights reserved.

3-D Warping in Four-Bar Laminated Linkages

This paper deals with the evaluation of the component-laminate load-carrying capacity, i.e., to calculate the loads that cause the failure of the individual layers and the component-laminate as a whole in four-bar mechanism. The component-laminate load-carrying capacity is evaluated using the Tsai-Wu-Hahn failure criterion for various layups. The reserve factor of each ply in the component-laminate is calculated by using the maximum resultant force and the maximum resultant moment occurring at different time steps at the joints of the mechanism. Here, all component bars of the mechanism are made of fiber reinforced laminates and have thin rectangular cross-sections. They could, in general, be pre-twisted and/or possess initial curvature, either by design or by defect. They are linked to each other by means of revolute joints. We restrict ourselves to linear materials with small strains within each elastic body (beam). Each component of the mechanism is modeled as a beam based on geometrically nonlinear 3-D elasticity theory. The component problems are thus split into 2-D analyses of reference beam cross-sections and nonlinear 1-D analyses along the three beam reference curves. For the thin rectangular cross-sections considered here, the 2-D cross-sectional nonlinearity is also overwhelming. This can be perceived from the fact that such sections constitute a limiting case between thin-walled open and closed sections, thus inviting the nonlinear phenomena observed in both. The strong elastic couplings of anisotropic composite laminates complicate the model further. However, a powerful mathematical tool called the Variational Asymptotic Method (VAM) not only enables such a dimensional reduction, but also provides asymptotically correct analytical solutions to the nonlinear cross-sectional analysis. Such closed-form solutions are used here in conjunction with numerical techniques for the rest of the problem to predict more quickly and accurately than would otherwise be possible. Local 3-D stress, strain and displacement fields for representative sections in the component-bars are recovered, based on the stress resultants from the 1-D global beam analysis. A numerical example is presented which illustrates the failure of each component-laminate and the mechanism as a whole.

Soft-chemical synthesis of new non-linear optical materials, K0.5M0.5Ti0.5OPO4(M = Nb, Ta),related to KTiOPO4

Soft-chemical oxidation of KTiOPO4-like KM(0.5)(V)Ti(0.5)(III)OPO(4) (M = Nb, Ta) using chlorine in CHCl3 is accompanied by partial deintercalation of potassium, yielding K(0.5)MV(0.5)Ti(0.5)(IV)OPO(4) compounds which are new non-linear optical materials that exhibit efficient second-harmonic generation of 1064 nm radiation, as does KTiOPO4.

Anomalous X-ray scattering study of local structures in the superionic conducting class (CuI)(0.3)(Cu2O)(0.35)(MoO3)(0.35)

The anomalous X-ray scattering (AXS) method using Cu and Mo K absorption edges has been employed for obtaining the local structural information of superionic conducting glass having the composition (CuI)(0.3)(Cu2O)(0.35)(MoO3)(0.35). The possible atomic arrangements in near-neighbor region of this glass were estimated by coupling the results with the least-squares analysis so as to reproduce two differential intensity profiles for Cu and Mo as well as the ordinary scattering profile. The coordination number of oxygen around Mo is found to be 6.1 at the distance of 0.187 nm. This implies that the MoO6 octahedral unit is a more probable structural entity in the glass rather than MoO4 tetrahedra which has been proposed based on infrared spectroscopy. The pre-peak shoulder observed at about 10 nm(-1) may be attributed to density fluctuation originating from the MoO6 octahedral units connected with the corner sharing linkage, in which the correlation length is about 0.8 nm. The value of the coordination number of I- around Cu+ is estimated as 4.3 at 0.261 nm, suggesting an arrangement similar to that in molten CuI.

Analysis of a cracked lug loaded by an interference fit pin

In the present study, a lug joint fitted with an interference fit (oversized) pin is considered with radial through cracks situated at diametrically opposite points perpendicular to the loading direction. A finite element contact stress algorithm is developed with linear elastic assumptions to deal with varying partial contact/separation at the pin-plate interface using a marching solution. Stress Intensity Factor (SIF) at the crack tips is evaluated using the Modified Crack Closure Integral (MCCI) method. The effect of change in crack length and edge distance on the load-contact relation, SIFs and stress distributions are studied. A rigorous plane stress elasticity solution of the pin-plate interface at the crack mouth confirmed the existence of the stress concentration leading to a local peak in the radial stress at the crack mouth and provided a method of estimating it quantitatively. Copyright (C) 1996 Elsevier Science Ltd.

Local polynomial convexity of the union of two totally-real surfaces at their intersection

We consider the following question: Let S (1) and S (2) be two smooth, totally-real surfaces in C-2 that contain the origin. If the union of their tangent planes is locally polynomially convex at the origin, then is S-1 boolean OR S-2 locally polynomially convex at the origin? If T (0) S (1) a (c) T (0) S (2) = {0}, then it is a folk result that the answer is yes. We discuss an obstruction to the presumed proof, and provide a different approach. When dim(R)(T0S1 boolean AND T0S2) = 1, we present a geometric condition under which no consistent answer to the above question exists. We then discuss conditions under which we can expect local polynomial convexity.

Linear and nonlinear optical properties of cumulenes and polyenynes: a model exact study

Model exact static and frequency-dependent polarizabilities, static second hyperpolarizabilities and THG coefficents of cumulenes and polyenynes, calculated within the correlated Pariser-Parr-Pople (PPP) model defined over the pi-framework are reported and compared with the results for the polyenes. It is found that for the same chain length, the polarizabilities and THG coefficients of the cumulenes are largest and those of the polyenynes smallest with the polyenes having an intermediate value. The optical gap of the infinite cumulene is lowest (0.75 eV) and is associated with a low transition dipole moment for an excitation involving transfer of an electron between the two orthogonal conjugated pi-systems. The polyenynes have the largest optical gap (4.37 eV), with the magnitude being nearly independent of the chain length. This excitation involves charge transfer between the conjugated bonds in the terminal triple bond. Chain length and frequency dependence of alpha(ij) and gamma(ijkl) of these systems are also reported. The effect of a heteroatom on the polarizability and THG coefficients of acetylenic systems is also reported. It has been found that the presence of the heteroatom reduces the polarizability and THG coefficients of these systems, an effect opposite to that found in the polyenes and cyanine dyes. This result has been associated with the different nature of the charge transfer in the acetylenic systems.

Linear electro-optic effect and temperature coefficient of birefringence in 4-nitro-4script-methylbenzylidene aniline single crystals

A study of the linear electro?optic effect in single crystals of the organic compound, 4?nitro�4??methylbenzylidene aniline is reported. The reduced half?wave voltages have been found to have values 2.8, 1.3, and 1.1 kV at 632.8, 514.5, and 488.0 nm, respectively and the corresponding values of the largest linear electro?optic coefficient have been calculated. The thermal variation of the birefringence has also been investigated and the temperature variation of the refractive index difference is found to have the value, d?n/dT = 15.8 × 10?5 K?1.

Linear dynamics and active control of an elastically supported travelling string

In this paper, the linear dynamics and active control of a string travelling with uniform velocity is presented. Discrete elastic supports are introduced along the length of the string. Finite element formulation is adopted to obtain the governing equations of motion. The velocity of translation introduces gyroscopic terms in the system equations. The effect of translation and the discrete elastic supports on the free vibration solution is studied. The solution is utilized in actively controlling the string vibrations due to an initial disturbance. The control, affected in modal space, is optimal with respect to a quadratic performance index. Numerical results are presented to demonstrate the effectiveness of the control strategy in regulating the travelling string vibrations.

Molecular interpretation of the linear relationship between the entropy and the enthalpy of activation of charge transfer reactions in polar liquids

The well-known linear relationship (T?S# =??H# +?, where 1 >? > 0,? > 0) between the entropy (?S#) and the enthalpy (?H#) of activation for reactions in polar liquids is investigated by using a molecular theory. An explicit derivation of this linear relation from first principles is presented for an outersphere charge transfer reaction. The derivation offers microscopic interpretation for the quantities? and?. It has also been possible to make connection with and justify the arguments of Bell put forward many years ago.