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.

Unsteady nonsimilar two-dimensional and axisymmetric water boundary layers with variable viscosity and prandtl number

The influence of temperature-dependent viscosity and Prandtl number on the unsteady laminar nonsimilar forced convection flow over two-dimensional and axisymmetric bodies has been examined where the unsteadiness and (or) nonsimilarity are (is) due to the free stream velocity, mass transfer, and transverse curvature. The partial differential equations governing the flow which involve three independent variables have been solved numerically using an implicit finite-difference scheme along with a quasilinearization technique. It is found that both the skin friction and heat transfer strongly respond to the unsteady free stream velocity distributions. The unsteadiness and injection cause the location of zero skin friction to move upstream. However, the effect of variable viscosity and Prandtl number is to move it downstream. The heat transfer is found to depend strongly on viscous dissipation, but the skin friction is little affected by it. In general, the results pertaining to variable fluid properties differ significantly, from those of constant fluid properties.

Variable density approach for rotating shallow shell of variable thickness

A new approach based on variable density in conjunction with shallow shell theory is proposed to analyse rotating shallow shell of variable thickness. Coupled non-linear ordinary differential equations governing shallows shells of variable thickness are first derived before applying the variable density approach. Results obtained from the new approach compare well with FEM calculation for a wide range of profiles considered in this paper.

Variable Sparsity Kernel Learning

This paper(1) presents novel algorithms and applications for a particular class of mixed-norm regularization based Multiple Kernel Learning (MKL) formulations. The formulations assume that the given kernels are grouped and employ l(1) norm regularization for promoting sparsity within RKHS norms of each group and l(s), s >= 2 norm regularization for promoting non-sparse combinations across groups. Various sparsity levels in combining the kernels can be achieved by varying the grouping of kernels-hence we name the formulations as Variable Sparsity Kernel Learning (VSKL) formulations. While previous attempts have a non-convex formulation, here we present a convex formulation which admits efficient Mirror-Descent (MD) based solving techniques. The proposed MD based algorithm optimizes over product of simplices and has a computational complexity of O (m(2)n(tot) log n(max)/epsilon(2)) where m is no. training data points, n(max), n(tot) are the maximum no. kernels in any group, total no. kernels respectively and epsilon is the error in approximating the objective. A detailed proof of convergence of the algorithm is also presented. Experimental results show that the VSKL formulations are well-suited for multi-modal learning tasks like object categorization. Results also show that the MD based algorithm outperforms state-of-the-art MKL solvers in terms of computational efficiency.

The effect of surface mass transfer on buoyancy induced flow in a variable porosity medium adjacent to a vertical heated plate

The effect of surface mass transfer on buoyancy induced flow in a variable porosity medium adjacent to a heated vertical plate is studied for high Rayleigh numbers. Similarity solutions are obtained within the frame work of boundary layer theory for a power law variation in surface temperature,T Wpropx lambda and surface injectionv Wpropx(lambda–1/2). The analysis incorporates the expression connecting porosity and permeability and also the expression connecting porosity and effective thermal diffusivity. The influence of thermal dispersion on the flow and heat transfer characteristics are also analysed in detail. The results of the present analysis document the fact that variable porosity enhances heat transfer rate and the magnitude of velocity near the wall. The governing equations are solved using an implicit finite difference scheme for both the Darcy flow model and Forchheimer flow model, the latter analysis being confined to an isothermal surface and an impermeable vertical plate. The influence of the intertial terms in the Forchheimer model is to decrease the heat transfer and flow rates and the influence of thermal dispersion is to increase the heat transfer rate.

Variable-speed wind power generation using doubly fed wound rotor induction machine - A comparison with alternative schemes

In this paper, a wind energy conversion system (WECS) using grid-connected wound rotor induction machine controlled from the rotor side is compared with both fixed speed and variable speed systems using cage rotor induction machine. The comparison is done on the basis of (I) major hardware components required, (II) operating region, and (III) energy output due to a defined wind function using the characteristics of a practical wind turbine. Although a fixed speed system is more simple and reliable, it severely limits the energy output of a wind turbine. In case of variable speed systems, comparison shows that using a wound rotor induction machine of similar rating can significantly enhance energy capture. This comes about due to the ability to operate with rated torque even at supersynchronous speeds; power is then generated out of the rotor as well as the stator. Moreover, with rotor side control, the voltage rating of the power devices and dc bus capacitor bank is reduced. The size of the line side inductor also decreasesd. Results are presented to show the substantial advantages of the doubly fed system.

Variable temperature x-ray crystal structure analysis of a type I langbeinite: Rb2Cd2(SO4)(3)

The structure of a type I langbeinite, Rb2Cd2(SO4)(3), displays three different phases, cubic with a = 10.378(5) Angstrom (space group P2(1)3) at room temperature, monoclinic at 120 K with a = 10.328(3), b = 10.322(3), c = 10.325(3) Angstrom, beta = 89.975(1)degrees (space group P2(1)), and orthorhombic at 85 K with a = 10.319(2), b = 10.321(2), c = 10.320(2) Angstrom (space group P2(1)2(1)2(1)), respectively. Precise single-crystal analyses of these phases indicate that Rb2Cd2(SO4)(3) distorts initially from cubic to monoclinic upon cooling followed by a significant reorientation of the SO4 tetrahedra, resulting in an orthorhombic symmetry upon further cooling. The three structures have been established unequivocally using the same crystal. There is no indication of the formation of an intermediate triclinic phase or any lattice disorder as conjectured in several earlier reports on compounds belonging to the type I langbeinite. The bond valence sum analyses of the coordination around the Rb sites indicate asymmetry in the bond strengths which could be the driving force of the ferroelectric behavior in these materials.

A method of tracking the peak power points for a variable speed wind energy conversion system

In this paper, a method of tracking the peak power in a wind energy conversion system (WECS) is proposed, which is independent of the turbine parameters and air density. The algorithm searches for the peak power by varying the speed in the desired direction. The generator is operated in the speed control mode with the speed reference being dynamically modified in accordance with the magnitude and direction of change of active power. The peak power points in the P-omega curve correspond to dP/domega = 0. This fact is made use of in the optimum point search algorithm. The generator considered is a wound rotor induction machine whose stator is connected directly to the grid and the rotor is fed through back-to-back pulse-width-modulation (PWM) converters. Stator flux-oriented vector control is applied to control the active and reactive current loops independently. The turbine characteristics are generated by a dc motor fed from a commercial dc drive. All of the control loops are executed by a single-chip digital signal processor (DSP) controller TMS320F240. Experimental results show that the performance of the control algorithm compares well with the conventional torque control method.

Low-temperature polaronic relaxations with variable range hopping conductivity in FeTiMO(6) (M = Ta,Nb,Sb)

Low-temperature dielectric measurements on FeTiMO(6) (M = Ta,Nb,Sb) rutile-type oxides at frequencies from 0.1 Hz to 10 MHz revealed anomalous dielectric relaxations with frequency dispersion. Unlike the high-temperature relaxor response of these materials, the low-temperature relaxations are polaronic in nature. The relationship between frequency and temperature of dielectric loss peak follows T(-1/4) behavior. The frequency dependence of ac conductivity shows the well-known universal dielectric response, while the dc conductivity follows Mott variable range hopping (VRH) behavior, confirming the polaronic origin of the observed dielectric relaxations. The frequency domain analysis of the dielectric spectra shows evidence for two relaxations, with the high-frequency relaxations following Mott VRH behavior more closely. Significantly, the Cr- and Ga-based analogs, CrTiNbO(6) and GaTiMO(6) (M = Ta,Nb), that were also studied, did not show these anomalies.

Best Node Selection Through Distributed Fast Variable Power Multiple Access

In many wireless applications, it is highly desirable to have a fast mechanism to resolve or select the packet from the user with the highest priority. Furthermore, individual priorities are often known only locally at the users. In this paper we introduce an extremely fast, local-information-based multiple access algorithm that selects the best node in 1.8 to 2.1 slots,which is much lower than the 2.43 slot average achieved by the best algorithm known to date. The algorithm, which we call Variable Power Multiple Access Selection (VP-MAS), uses the local channel state information from the accessing nodes to the receiver, and maps the priorities into the receive power.It is inherently distributed and scales well with the number of users. We show that mapping onto a discrete set of receive power levels is optimal, and provide a complete characterization for it. The power levels are chosen to exploit packet capture that inherently occurs in a wireless physical layer. The VP-MAS algorithm adjusts the expected number of users that contend in each step and their respective transmission powers, depending on whether previous transmission attempts resulted in capture,idle channel, or collision.

An improved sapce phasor based current hysteresis controller with reduced switching frequency variations using variable parabolic bands

A current error space phasor based simple hysteresis controller is proposed in this paper to control the switching frequency variation in two-level pulsewidth-modulation (PWM) inverter-fed induction motor (IM) drives. A parabolic boundary for the current error space phasor is suggested for the first time to obtain the switching frequency spectrum for output voltage with hysteresis controller similar to the constant switching frequency voltage-controlled space vector PWM-based IM drive. A novel concept of online variation of this parabolic boundary, which depends on the operating speed of motor, is presented. A generalized technique that determines the set of unique parabolic boundaries for a two-level inverter feeding any given induction motor is described. The sector change logic is self-adaptive and is capable of taking the drive up to the six-step mode if needed. Steady-state and transient performance of proposed controller is experimentally verified on a 3.7-kW IM drive in the entire speed range. Close resemblance of the simulation and experimental results is shown.

Pricing a Shared Access Link for Fair and Efficient Operation with Variable User Data Rates

The literature on pricing implicitly assumes an "infinite data" model, in which sources can sustain any data rate indefinitely. We assume a more realistic "finite data" model, in which sources occasionally run out of data; this leads to variable user data rates. Further, we assume that users have contracts with the service provider, specifying the rates at which they can inject traffic into the network. Our objective is to study how prices can be set such that a single link can be shared efficiently and fairly among users in a dynamically changing scenario where a subset of users occasionally has little data to send. User preferences are modelled by concave increasing utility functions. Further, we introduce two additional elements: a convex increasing disutility function and a convex increasing multiplicative congestion-penally function. The disutility function takes the shortfall (contracted rate minus present rate) as its argument, and essentially encourages users to send traffic at their contracted rates, while the congestion-penalty function discourages heavy users from sending excess data when the link is congested. We obtain simple necessary and sufficient conditions on prices for fair and efficient link sharing; moreover, we show that a single price for all users achieves this. We illustrate the ideas using a simple experiment.