Modeling of angiogenin-3 '-NMP complex

Angiogenin belongs to the Ribonuclease superfamily and has a weak enzymatic activity that is crucial for its biological function of stimulating blood vessel growth. Structural studies on ligand bound Angiogenin will go a long way in understanding the mechanism of the protein as well as help in designing drugs against it. In this study we present the first available structure of nucleotide ligand bound Angiogenin obtained by computer modeling. The importance of this study in itself notwithstanding, is a precursor to modeling a full dinucleotide substrate onto Angiogenin. Bovine Angiogenin, the structure of which has been solved at a high resolution, was earlier subjected to Molecular Dynamics simulations for a nanosecond. The MD structures offer better starting points for docking as they offer lesser obstruction than the crystal structure to ligand binding. The MD structure with the least serious short contacts was modeled to obtain a steric free Angiogenin - 3' mononucleotide complex structure. The structures were energetically minimized and subjected to a brief spell of Molecular Dynamics. The results of the simulation show that all the li,ligand-Angiogenin interactions and hydrogen bonds are retained, redeeming the structure and docking procedure. Further, following ligand - protein interactions in the case of the ligands 3'-CMP and 3'-UMP we were able to speculate on how Angiogenin, a predominantly prymidine specific ribonuclease prefers Cytosine to Uracil in the first base position.

Thermodynamic properties of LaFeO3-delta and LaFe12O19

The standard Gibbs energies of formation of lanthanum orthoferrite (LaFeO3-delta) and hexaferrite (LaFe12O19)were determined using solid-state electrochemical cells incorporating yttria-stabilized zirconia as the electrolyte and pure oxygen gas at ambient pressure as the reference electrode. From emf of the solid-state cell, the Gibbs energy of formation of nonstoichiometric orthoferrite (LaFeO3-delta) is obtained. To derive values for the stoichiometric phase, variation of the oxygen nonstoichiometric parameter with oxygen partial pressure was measured using thermogravimetry under controlled gas mixtures. The results obtained for LaFeO3 and LaFe12O19 can be summarized by the following equations, which represent the formation of ternary oxides from their component binary oxides: 1/2 La2O3 + 1/2 Fe2O3 -> LaFeO3: Delta G degrees (LaFeO3) (+/- 450) (J mol(-1)) = -62920 - 2.12T (K), and 1/2 La2O3 + 9/2Fe(2)O(3) + Fe3O4 -> LaFe12O19; Delta G degrees (LaFe12O19) (+/- 200) (J mol(-1)) = -103900 + 21.25T (K). These data are discussed critically in comparison with thermodynamic values reported in the literature from a variety of measurements. The values obtained in this study are consistent with calorimetric entropy and enthalpy of formation of the perovskite phase and with some of the Gibbs energy measurements reported in the literature. For the lanthanum hexaferrite (LaFe12O19) there are no prior thermodynamic measurements for comparison. (c) 2011 Elsevier B.V. All rights reserved.

Modeling of precipitation in reverse micellar systems

A model of the precipitation process in reverse micelles has been developed to calculate the size of fine particles obtained therein. While the method shares several features of particle nucleation and growth common to precipitation in large systems, complexities arise in describing the processes of nucleation, due to the extremely small size of a micelle and of particle growth caused by fusion among the micelles. Occupancy of micelles by solubilized molecules is governed by Poisson statistics, implying most of them are empty and cannot nucleate of its own. The model therefore specifies the minimum number of solubilized molecules required to form a nucleus which is used to calculate the homogeneous nucleation rate. Simultaneously, interaction between micelles is assumed to occur by Brownian collision and instantaneous fusion. Analysis of time scales of various events shows growth of particles to be very fast compared to other phenomena occurring. This implies that nonempty micelles either are supersaturated or contain a single precipitated particle and allows application of deterministic population balance equations to describe the evolution of the system with time. The model successfully predicts the experimental measurements of Kandori ct al.(3) on the size of precipitated CaCO3 particles, obtained by carbonation of reverse micelles containing aqueous Ca(OH)(2) solution.

Modeling of the cooling process on the runout table of a hot strip mill - A parallel approach

This paper deals with the development of a new model for the cooling process on the runout table of hot strip mills, The suitability of different numerical methods for the solution of the proposed model equation from the point of view of accuracy and computation time are studied, Parallel solutions for the model equation are proposed.

Petri net-based modeling of a class of complex digital systems

We present through the use of Petri Nets, modeling techniques for digital systems realizable using FPGAs. These Petri Net models are used for logic validation at the logic design phase. The technique is illustrated by modeling practical circuits. Further, the utility of the technique with respect to timing analysis of the modeled digital systems is considered. Copyright (C) 1997 Elsevier Science Ltd

Representation of thermodynamic properties of quaternary systems using interaction parameters

Integral excess free energy of a quaternary system has been expressed in terms of the MacLaurin infinite series. The series is subjected to appropriate boundary conditions and each of the derivatives correlated to the corresponding interaction coefficients. The derivation of the partial functions involves extensive summation of various infinite series pertaining to the first order and quaternary parameters to remove any truncational error. The thermodynamic consistency of the derived partials has been established based on the Gibbs-Duhem relations. The equations are used to interpret the thermodynamic properties of the Fe-Cr-Ni-N system.

Analysis, Design, Modeling, and Implementation of an Active Clamp HF Link Converter

This paper deals with the system oriented analysis, design, modeling, and implementation of active clamp HF link three phase converter. The main advantage of the topology is reduced size, weight, and cost of the isolation transformer. However, violation of basic power conversion rules due to presence of the leakage inductance in the HF transformer causes over voltage stresses across the cycloconverter devices. It makes use of the snubber circuit necessary in such topologies. The conventional RCD snubbers are dissipative in nature and hence inefficient. The efficiency of the system is greatly improved by using regenerative snubber or active clamp circuit. It consists of an active switching device with an anti-parallel diode and one capacitor to absorb the energy stored in the leakage inductance of the isolation transformer and to regenerate the same without affecting circuit performance. The turn on instant and duration of the active device are selected such that it requires simple commutation requirements. The time domain expressions for circuit dynamics, design criteria of the snubber capacitor with two conflicting constrains (over voltage stress across the devices and the resonating current duration), the simulation results based on generalized circuit model and the experimental results based on laboratory prototype are presented.

Thermodynamic constraints along isograms in ternary systems: application to three-phase equilibria

Thermodynamic constraints on component chemical potentials in three-phase fields introduced by the various isograms suggested in the literature are derived for a ternary system containing compounds. When compositions of two compounds lie on an isogram, it is associated with specific characteristics which can be used to obtain further understanding of the interplay of thermodynamic factors that determine phase equilibria. When two compounds are shared by adjacent three-phase fields, the constraints are dictated by binary compositions generated by the intersection of a line passing through the shared compounds with the sides of the ternary triangle. Generalized expressions for an arbitrary line through the triangle are presented. These are consistent with special relations obtained along Kohler, Colinet and Jacob isograms. Five axioms are introduced and proved. They provide valuable tools for checking consistency of thermodynamic measurements and for deriving thermodynamic properties from phase diagrams. (C) 1997 Elsevier Science S.A.

Absolute Entropy and Energy of Carbon Dioxide Using the Two-Phase Thermodynamic Model

The two-phase thermodynamic (2PT) model is used to determine the absolute entropy and energy of carbon dioxide over a wide range of conditions from molecular dynamics trajectories. The 2PT method determines the thermodynamic properties by applying the proper statistical mechanical partition function to the normal modes of a fluid. The vibrational density of state (DoS), obtained from the Fourier transform of the velocity autocorrelation function, converges quickly, allowing the free energy, entropy, and other thermodynamic properties to be determined from short 20-ps MD trajectories. The anharmonic effects in the vibrations are accounted for by the broadening of the normal modes into bands from sampling the velocities over the trajectory. The low frequency diffusive modes, which lead to finite DoS at zero frequency, are accounted for by considering the DoS as a superposition of gas-phase and solid-phase components (two phases). The analytical decomposition of the DoS allows for an evaluation of properties contributed by different types of molecular motions. We show that this 2PT analysis leads to accurate predictions of entropy and energy of CO2 over a wide range of conditions (from the triple point to the critical point of both the vapor and the liquid phases along the saturation line). This allows the equation of state of CO2 to be determined, which is limited only by the accuracy of the force field. We also validated that the 2PT entropy agrees with that determined from thermodynamic integration, but 2PT requires only a fraction of the time. A complication for CO2 is that its equilibrium configuration is linear, which would have only two rotational modes, but during the dynamics it is never exactly linear, so that there is a third mode from rotational about the axis. In this work, we show how to treat such linear molecules in the 2PT framework.

Micromechanical modeling of granular materials: effect of confining pressure on mechanical behavior

This paper reports the effect of confining pressure on the mechanical behavior of granular materials from micromechanical considerations starting from the grain scale level, based on the results of numerically simulated tests on disc assemblages using discrete element modeling (DEM). The two macro parameters which are influenced by the increase in confining pressure are stiffness (increases) and volume change (decreases). The lateral strain coefficient (Poisson's ratio) at the beginning of the test is more or less constant. The angle of internal friction slightly decreases with increase in confining pressure. The numerical results of disc assemblages indicate very clearly a non-linear Mohr-Coulomb failure envelope with increase in confining pressure. The increase in average coordination number and accompanying decrease of fabric anisotropy reduce the shear strength at higher confining pressures. Micromechanical explanations of the macroscopic behavior are presented in terms of the force and fabric anisotropy coefficients. (C) 1999 Elsevier Science Ltd. AII rights reserved.

Modeling and control of unified power flow controller for transient stability

FACTS controllers are emerging as viable and economic solutions to the problems of large interconnected ne networks, which can endanger the system security. These devices are characterized by their fast response, absence of inertia, and minimum maintenance requirements. Thyristor controlled equipment like Thyristor Controlled Series Capacitor (TCSC), Static Var Compensator (SVC), Thyristor Controlled Phase angle Regulator (TCPR) etc. which involve passive elements result in devices of large sizes with substantial cost and significant labour for installation. An all solid-state device using GTOs leads to reduction in equipment size and has improved performance. The Unified Power Flow Controller (UPFC) is a versatile controller which can be used to control the active and reactive power in the Line independently. The concept of UPFC makes it possible to handle practically all power flow control and transmission line compensation problems, using solid-state controllers, which provide functional flexibility, generally not attainable by conventional thyristor controlled systems. In this paper, we present the development of a control scheme for the series injected voltage of the UPFC to damp the power oscillations and improve transient stability in a power system. (C) 1998 Elsevier Science Ltd. All rights reserved.

Stochastic dynamics modeling of the protein sequence length distribution in genomes: implications for microbial evolution

In this paper, we report an analysis of the protein sequence length distribution for 13 bacteria, four archaea and one eukaryote whose genomes have been completely sequenced, The frequency distribution of protein sequence length for all the 18 organisms are remarkably similar, independent of genome size and can be described in terms of a lognormal probability distribution function. A simple stochastic model based on multiplicative processes has been proposed to explain the sequence length distribution. The stochastic model supports the random-origin hypothesis of protein sequences in genomes. Distributions of large proteins deviate from the overall lognormal behavior. Their cumulative distribution follows a power-law analogous to Pareto's law used to describe the income distribution of the wealthy. The protein sequence length distribution in genomes of organisms has important implications for microbial evolution and applications. (C) 1999 Elsevier Science B.V. All rights reserved.

Thermodynamic properties of the calcium ferrites CaFe2O4 and Ca2Fe2O5

The chemical potentials of CaO in the two-phase fields Fe2O3 + CaFe2O4 and CaFe2O4 + Ca2Fe2O5 of the pseudobinary system CaO - Fe2O3 have been measured in the temperature range from 975 to 1275 K, relative to pure CaO as the reference state, using solid state galvanic cells incorporating single-crystal CaF2 as the solid electrolyte. The cell was operated under pure oxygen at ambient pressure. The standard Gibbs energies of formation of calcium ferrites, CaFe2O4 and Ca2Fe2O5, were derived from the reversible emfs. The results can be summarized by the following equations:CaO + Fe2O3 --> CaFe2O4;Delta G degrees = - 37,480 + 1.16 T (+/- 250) J/mol 2 CaO + Fe2O3 --> Ca2Fe2O5;Delta G degrees = - 45, 280 - 13.51 T (+/- 275) J/mol These values are compared with thermodynamic data reported in the literature. The results of this study are in excellent agreement with heat capacity data, and in reasonable agreement with earlier measurements of enthalpy and Gibbs energy of formation, but suggest significant revision of enthalpies of formation of calcium ferrites given in current thermodynamic compilations.

Modeling of concrete cracking-A hybrid technique of using displacement discontinuity element method and direct boundary element method

This paper presents a new approach by making use of a hybrid method of using the displacement discontinuity element method and direct boundary element method to model concrete cracking by incorporating fictitious crack model. Fracture mechanics approach is followed using the Hillerborg's fictitious crack model. A boundary element based substructure method and a hybrid technique of using displacement discontinuity element method and direct boundary element method are compared in this paper. In order to represent the process zone ahead of the crack, closing forces are assumed to act in such a way that they obey a linear normal stress-crack opening displacement law. Plain concrete beams with and without initial crack under three-point loading were analyzed by both the methods. The numerical results obtained were shown to agree well with the results from existing finite element method. The model is capable of reproducing the whole range of load-deflection response including strain-softening and snap-back behavior as illustrated in the numerical examples. (C) 2011 Elsevier Ltd. All rights reserved.

Large eddy simulation of a premixed flame with approximate deconvolution modeling

Approximate deconvolution modeling is a very recent approach to large eddy simulation of turbulent flows. It has been applied to compressible flows with success. Here, a premixed flame which forms in the wake of a flameholder has been selected to examine the subgrid-scale modeling of reaction rate by this new method because a previous plane two-dimensional simulation of this wake flame, using a wrinkling function and artificial flame thickening, had revealed discrepancies when compared with experiment. The present simulation is of the temporal evolution of a round wakelike flow at two Reynolds numbers, Re = 2000 and 10,000, based on wake defect velocity and wake diameter. A Fourier-spectral code has been used. The reaction is single-step and irreversible, and the rate follows an Arrhenius law. The reference simulation at the lower Reynolds number is fully resolved. At Re = 10,000, subgrid-scale contributions are significant. It was found that subgrid-scale modeling in the present simulation agrees more closely with unresolved subgrid-scale effects observed in experiment. Specifically, the highest contributions appeared in thin folded regions created by vortex convection. The wrinkling function approach had not selected subgrid-scale effects in these regions.