The mean geometry of the peptide unit from crystal structure data

The average dimensions of the peptide unit have been obtained from the data reported in recent crystal structure analyses of di- and tripeptides. The bond lengths and bond angles agree with those in common use, except for the bond angle C---N---H, which is about 4° less than the accepted value, and the angle C2α---N---H which is about 4° more. The angle τ (Cα) has a mean value of 114° for glycyl residues and 110° for non-glycyl residues. Attention is directed to these mean values as observed in crystal structures, as they are relevant for model building of peptide chain structures.

Kinetic characterization of rat brain type IIA sodium channel alpha-subunit stably expressed in a somatic cell line

1. The rat brain type IIA Na+ channel alpha-subunit was stably expressed in Chinese hamster ovary (CHO) cells. Current through the expressed Na+ channels was studied using the whole-cell configuration of the patch clamp technique. The transient Na+ current was sensitive to TTX and showed a bell-shaped peak current vs. membrane potential relation. 2. Na+ current inactivation was better described by the sum of two exponentials in the potential range -30 to +40 mV, with. a dominating fast component and a small slower component. 3. The steady-state inactivation, h(infinity), was related to potential by a Boltzmann distribution, underlying thr ee states of the inactivation gate. 4. Recovery of the channels from inactivation at different potentials in the range -70 to -120 mV were characterized by al? initial delay which decreased with hyperpolarization. The time course was well fitted by the sum of two exponentials. In this case the slower exponential was the major component, and both time constants decreased with hyperpolarization. 5. For a working description of the Na+ channel inactivation in this preparation, with a minimal deviation from the Hodgkin-Huxley model, a three-state scheme of the form O reversible arrow I-1 reversible arrow I-2 was proposed, replacing the original two-state scheme of the Hodgkin-Huxley model, and the rate constants are reported. 6. The instantaneous current-voltage relationship showed marked deviation from linearity and was satisfactorily fitted by the constant-field equation. 7. The time course of activation was described by an m(x) model. However, the best-fitted value of x varied with the membrane potential and had a mean value of 2. 8. Effective gating charge was determined to be 4.7e from the slope of the activation plot, plotted on a logarithmic scale. 9. The rate constants of activation, alpha(m) and beta(m), were determined. Their functional dependence on the membrane potential was investigated.

Determination of the thermodynamic stability of TiB2

The standard free energy of formation of titanium boride (TiB2) Was measured by the Electro Motive Force (EMF) method (by using yttria doped thoria (YDT) as the solid electrolyte). Two galvanic cells viz. Cell (I): Pt, TiB2 (s), TiO2 (s), B (s) vertical bar YDT vertical bar NiO (s), Ni (s), Pt and cell (II): Pt, TiB2 (s), TiO2 (s), B (s) vertical bar YDT vertical bar FeO (s). Fe (s), Pt were constructed in order to determine the Delta(f)G degrees, of TiB2. Enthalpy increments on TiB2 were measured by using inverse drop calorimetry over the temperature range 583-1769 K. The heat capacity, entropy and the free energy function have been derived from these experimental data in the temperature range 298-1800 K. The mean value of the standard enthalpy of formation of TiB2 (Delta H-f(298)degrees (TiB2)) was obtained by combining these Delta(f)G degrees, values and the free energy functions of TiB2 derived from the drop calorimetry data. The mean values of Delta H-f(298)degrees (TiB2) derived from the Delta(f)G degrees, data obtained from cell I and II were -322 +/- 1.2 kJ mol(-1) and -323.3 +/- 2.1 kJ mol(-1), respectively. These values were found to be in very good agreement with the assessed data. (C) 2009 Elsevier B.V. All rights reserved.

Dynamic simulation of activated sludge based wastewater treatment processes: Case studies with Titagarh Sewage Treatment Plant, India

STOAT has been extensively used for the dynamic simulation of an activated sludge based wastewater treatment plant in the Titagarh Sewage Treatment Plant, near Kolkata, India. Some alternative schemes were suggested. Different schemes were compared for the removal of Total Suspended Solids (TSS), b-COD, ammonia, nitrates etc. A combination of IAWQ#1 module with the Takacs module gave best results for the existing scenarios of the Titagarh Sewage Treatment Plant. The modified Bardenpho process was found most effective for reducing the mean b-COD level to as low as 31.4 mg/l, while the mean TSS level was as high as 100.98 mg/l as compared to the mean levels of TSS (92 62 mg/l) and b-COD (92.0 mg/l) in the existing plant. Scheme 2 gave a better scenario for the mean TSS level bringing it down to a mean value of 0.4 mg/l, but a higher mean value for the b-COD level at 54.89 mg/l. The Scheme Final could reduce the mean TSS level to 2.9 mg/l and the mean b-COD level to as low as 38.8 mg/l. The Final Scheme looks to be a technically viable scheme with respect to the overall effluent quality for the plant. (C) 2009 Elsevier B.V. All rights reserved.

Modeling server-unreliability in closed queuing-networks

A method is presented to model server unreliability in closed queuing networks. Breakdowns and repairs of servers, assumed to be time-dependent, are modeled using virtual customers and virtual servers in the system. The problem is thus converted into a closed queue with all reliable servers and preemptive resume priority centers. Several recent preemptive priority approximations and an approximation of the one proposed are used in the analysis. This method has approximately the same computational requirements as that of mean-value analysis for a network of identical dimensions and is therefore very efficient

A Cache coherence protocol for MIN-based multiprocessors

In this paper we present a cache coherence protocol for multistage interconnection network (MIN)-based multiprocessors with two distinct private caches: private-blocks caches (PCache) containing blocks private to a process and shared-blocks caches (SCache) containing data accessible by all processes. The architecture is extended by a coherence control bus connecting all shared-block cache controllers. Timing problems due to variable transit delays through the MIN are dealt with by introducing Transient states in the proposed cache coherence protocol. The impact of the coherence protocol on system performance is evaluated through a performance study of three phases. Assuming homogeneity of all nodes, a single-node queuing model (phase 3) is developed to analyze system performance. This model is solved for processor and coherence bus utilizations using the mean value analysis (MVA) technique with shared-blocks steady state probabilities (phase 1) and communication delays (phase 2) as input parameters. The performance of our system is compared to that of a system with an equivalent-sized unified cache and with a multiprocessor implementing a directory-based coherence protocol. System performance measures are verified through simulation.

Magnetic and spin evolution of pulsars

We explore the consequences of the model of spin-down-induced flux expulsion for the magnetic field evolution in solitary as well as in binary neutron stars. The spin evolution of pulsars, allowing for their field evolution according to this model, is shown to be consistent with the existing observational constraints in both low- and high-mass X-ray binary systems. The contribution from pulsars recycled in massive binaries to the observed excess in the number of low-field (10(11)-10(12) G) solitary pulsars is argued to be negligible in comparison with that of normal pulsars undergoing a 'restricted' field decay predicted by the adopted field decay model. Magnetic fields of neutron stars born in close binaries with intermediate- or high-mass main-sequence companions are predicted to decay down to values as low as similar to 10(6) G, which would leave them unobservable as pulsars during most of their lifetimes. The post-recycling evolution of some of these systems can, however, account for the observed binary pulsars having neutron star or massive white dwarf companions. Pulsars recycled in the disc population low-mass binaries are expected to have residual fields greater than or similar to 10(8) G, while for those processed in globular clusters larger residual fields are predicted because of the lower field strength of the neutron star at the epoch of binary formation. A value of tau similar to 1-2 x 10(7) yr for the mean value of the Ohmic decay time-scale in the crusts of neutron stars is suggested, based on the consistency of the model predictions with the observed distribution of periods and magnetic fields in the single and binary pulsars.

Stability of stochastic Leipholz column with stochastic loading

The Leipholz column which is having the Young modulus and mass per unit length as stochastic processes and also the distributed tangential follower load behaving stochastically is considered. The non self-adjoint differential equation and boundary conditions are considered to have random field coefficients. The standard perturbation method is employed. The non self-adjoint operators are used within the regularity domain. Full covariance structure of the free vibration eigenvalues and critical loads is derived in terms of second order properties of input random fields characterizing the system parameter fluctuations. The mean value of critical load is calculated using the averaged problem and the corresponding eigenvalue statistics are sought. Through the frequency equation a transformation is done to yield load parameter statistics. A numerical study incorporating commonly observed correlation models is reported which illustrates the full potentials of the derived expressions.

Lopsidedness in WHISP galaxies I. Rotation curves and kinematic lopsidedness

The frequently observed lopsidedness of the distribution of stars and gas in disc galaxies is still considered as a major problem in galaxy dynamics. It is even discussed as an imprint of the formation history of discs and the evolution of baryons in dark matter haloes. Here, we analyse a selected sample of 70 galaxies from the Westerbork Hi Survey of Spiral and Irregular Galaxies. The Hi data allow us to follow the morphology and the kinematics out to very large radii. In the present paper, we present the rotation curves and study the kinematic asymmetry. We extract the rotation curves of the receding and approaching sides separately and show that the kinematic behaviour of disc galaxies can be classified into five different types: symmetric velocity fields where the rotation curves of the receding and approaching sides are almost identical; global distortions where the rotation velocities of the receding and approaching sides have an offset that is constant with radius; local distortions leading to large deviations in the inner and negligible deviations in the outer parts (and vice versa); and distortions that divide the galaxies into two kinematic systems that are visible in terms of the different behaviour of the rotation curves of the receding and approaching sides, which leads to a crossing and a change in side. The kinematic lopsidedness is measured from the maximum rotation velocities, averaged over the plateau of the rotation curves. This gives a good estimate of the global lopsidedness in the outer parts of the sample galaxies. We find that the mean value of the perturbation parameter denoting the lopsided potential as obtained from the kinematic data is 0.056. Altogether, 36% of the sample galaxies are globally lopsided, which can be interpreted as the disc responding to a halo that was distorted by a tidal encounter. In Paper II, we study the morphological lopsidedness of the same sample of galaxies.

Power Efficient Redundant Execution for Chip Multiprocessor

This paper describes the design of a power efficient microarchitecture for transient fault detection in chip multiprocessors (CMPs) We introduce a new per-core dynamic voltage and frequency scaling (DVFS) algorithm for our architecture that significantly reduces power dissipation for redundant execution with a minimal performance overhead. Using cycle accurate simulation combined with a simple first order power model, we estimate that our architecture reduces dynamic power dissipation in the redundant core by an mean value of 79% and a maximum of 85% with an associated mean performance overhead of only 1:2%

Surrogate based design optimisation of composite aerofoil cross-section for helicopter vibration reduction

Design optimisation of a helicopter rotor blade is performed. The objective is to reduce helicopter vibration and constraints are put on frequencies and aeroelastic stability. The ply angles of the D-spar and skin of the composite rotor blade with NACA 0015 aerofoil section are considered as design variables. Polynomial response surfaces and space filling experimental designs are used to generate surrogate models of the objective function with respect to cross-section properties. The stacking sequence corresponding to the optimal cross-section is found using a real-coded genetic algorithm. Ply angle discretisation of 1 degrees, 15 degrees, 30 degrees and 45 degrees are used. The mean value of the objective function is used to find the optimal blade designs and the resulting designs are tested for variance. The optimal designs show a vibration reduction of 26% to 33% from the baseline design. A substantial reduction in vibration and an aeroelastically stable blade is obtained even after accounting for composite material uncertainty.

Methodology for Pavement Design Reliability and Back Analysis Using Markov Chain Monte Carlo Simulation

Given the increasing cost of designing and building new highway pavements, reliability analysis has become vital to ensure that a given pavement performs as expected in the field. Recognizing the importance of failure analysis to safety, reliability, performance, and economy, back analysis has been employed in various engineering applications to evaluate the inherent uncertainties of the design and analysis. The probabilistic back analysis method formulated on Bayes' theorem and solved using the Markov chain Monte Carlo simulation method with a Metropolis-Hastings algorithm has proved to be highly efficient to address this issue. It is also quite flexible and is applicable to any type of prior information. In this paper, this method has been used to back-analyze the parameters that influence the pavement life and to consider the uncertainty of the mechanistic-empirical pavement design model. The load-induced pavement structural responses (e.g., stresses, strains, and deflections) used to predict the pavement life are estimated using the response surface methodology model developed based on the results of linear elastic analysis. The failure criteria adopted for the analysis were based on the factor of safety (FOS), and the study was carried out for different sample sizes and jumping distributions to estimate the most robust posterior statistics. From the posterior statistics of the case considered, it was observed that after approximately 150 million standard axle load repetitions, the mean values of the pavement properties decrease as expected, with a significant decrease in the values of the elastic moduli of the expected layers. An analysis of the posterior statistics indicated that the parameters that contribute significantly to the pavement failure were the moduli of the base and surface layer, which is consistent with the findings from other studies. After the back analysis, the base modulus parameters show a significant decrease of 15.8% and the surface layer modulus a decrease of 3.12% in the mean value. The usefulness of the back analysis methodology is further highlighted by estimating the design parameters for specified values of the factor of safety. The analysis revealed that for the pavement section considered, a reliability of 89% and 94% can be achieved by adopting FOS values of 1.5 and 2, respectively. The methodology proposed can therefore be effectively used to identify the parameters that are critical to pavement failure in the design of pavements for specified levels of reliability. DOI: 10.1061/(ASCE)TE.1943-5436.0000455. (C) 2013 American Society of Civil Engineers.

Energy Hyperspace for Stacking Interaction in AU/AU Dinucleotide Step: Dispersion-Corrected Density Functional Theory Study

Double helical structures of DNA and RNA are mostly determined by base pair stacking interactions, which give them the base sequence-directed features, such as small roll values for the purine-pyrimidine steps. Earlier attempts to characterize stacking interactions were mostly restricted to calculations on fiber diffraction geometries or optimized structure using ab initio calculations lacking variation in geometry to comment on rather unusual large roll values observed in AU/AU base pair step in crystal structures of RNA double helices. We have generated stacking energy hyperspace by modeling geometries with variations along the important degrees of freedom, roll, and slide, which were chosen via statistical analysis as maximally sequence dependent. Corresponding energy contours were constructed by several quantum chemical methods including dispersion corrections. This analysis established the most suitable methods for stacked base pair systems despite the limitation imparted by number of atom in a base pair step to employ very high level of theory. All the methods predict negative roll value and near-zero slide to be most favorable for the purine-pyrimidine steps, in agreement with Calladine's steric clash based rule. Successive base pairs in RNA are always linked by sugar-phosphate backbone with C3-endo sugars and this demands C1-C1 distance of about 5.4 angstrom along the chains. Consideration of an energy penalty term for deviation of C1-C1 distance from the mean value, to the recent DFT-D functionals, specifically B97X-D appears to predict reliable energy contour for AU/AU step. Such distance-based penalty improves energy contours for the other purine-pyrimidine sequences also. (c) 2013 Wiley Periodicals, Inc. Biopolymers 101: 107-120, 2014.

Revisiting SW J2000.6+3210: a persistent Be X-ray pulsar?

We present a detailed timing and spectral analysis of the Be X-ray binary SW J2000.6+3210 discovered by the Burst Alert Telescope Galactic plane survey. Two Suzaku observations of the source made at six months interval, reveal pulsations at similar to 890 s for both observations with a much weaker pulse fraction in the second one. Pulsations are clearly seen in the energy band of 0.3-10 keV of X-ray Imaging Spectrometer for both observations and at high energies up to 40 keV for the second observation. The broad-band X-ray spectrum is consistent with a power-law and high-energy cut-off model along with a hot blackbody component. No change in spectral parameters is detected between the observations. We have also analysed several short observations of the source with Swift/XRT and detected only a few per cent variation in flux around a mean value of 3.5 x 10(-11) erg cm(-2) s(-1). The results indicate that SW J2000.6+3210 is a member of persistent Be X-ray binaries which have the same broad characteristics as this source.

Influence of Spatial Variability on Pavement Responses Using Latin Hypercube Sampling on Two-Dimensional Random Fields

Although uncertainties in material properties have been addressed in the design of flexible pavements, most current modeling techniques assume that pavement layers are homogeneous. The paper addresses the influence of the spatial variability of the resilient moduli of pavement layers by evaluating the effect of the variance and correlation length on the pavement responses to loading. The integration of the spatially varying log-normal random field with the finite-difference method has been achieved through an exponential autocorrelation function. The variation in the correlation length was found to have a marginal effect on the mean values of the critical strains and a noticeable effect on the standard deviation which decreases with decreases in correlation length. This reduction in the variance arises because of the spatial averaging phenomenon over the softer and stiffer zones generated because of spatial variability. The increase in the mean value of critical strains with decreasing correlation length, although minor, illustrates that pavement performance is adversely affected by the presence of spatially varying layers. The study also confirmed that the higher the variability in the pavement layer moduli, introduced through a higher value of coefficient of variation (COV), the higher the variability in the pavement response. The study concludes that ignoring spatial variability by modeling the pavement layers as homogeneous that have very short correlation lengths can result in the underestimation of the critical strains and thus an inaccurate assessment of the pavement performance. (C) 2014 American Society of Civil Engineers.