Physically consistent simulation of mesoscale chemical kinetics: The non-negative FIS-alpha method

Biochemical pathways involving chemical kinetics in medium concentrations (i.e., at mesoscale) of the reacting molecules can be approximated as chemical Langevin equations (CLE) systems. We address the physically consistent non-negative simulation of the CLE sample paths as well as the issue of non-Lipschitz diffusion coefficients when a species approaches depletion and any stiffness due to faster reactions. The non-negative Fully Implicit Stochastic alpha (FIS alpha) method in which stopped reaction channels due to depleted reactants are deleted until a reactant concentration rises again, for non-negativity preservation and in which a positive definite Jacobian is maintained to deal with possible stiffness, is proposed and analysed. The method is illustrated with the computation of active Protein Kinase C response in the Protein Kinase C pathway. (C) 2011 Elsevier Inc. All rights reserved.

Analysis of Lined Ducts With Mean Flow, With Application to Dissipative Mufflers

Mufflers with at least one acoustically absorptive duct are generally called dissipative mufflers. Generally, for want of systems approach, these mufflers are characterized by transmission loss of the lined duct with overriding corrections for the terminations, mean flow, etc. In this article, it is proposed that dissipative duct should be integrated with other muffler elements, source impedance and radiation impedance, by means of transfer matrix approach. Towards this end, the transfer matrix for rectangular duct with mean flow has been derived here, for the least attenuated mode. Mean flow introduces a coupling between transverse wave numbers and axial wave number, the evaluation of which therefore calls for simultaneous solution of two or three transcendental equations. This is done by means of a Newton-Raphson iteration scheme, which is illustrated here for square ducts lined with porous ceramic tiles.

Transfer matrix modeling of hyperbolic and parabolic ducts with incompressible mean flow

A general differential equation for the propagation of sound in a variable area duct or nozzle carrying incompressible mean flow (of low Mach number) is derived and solved for hyperbolic and parabolic shapes. Expressions for the state variables of acoustic pressure and acoustic mass velocity of the shapes are derived. Self‐consistent expressions for the four‐pole parameters are developed. The conical, exponential, catenoidal, sine, and cosine ducts are shown to be special cases of hyperbolic ducts. Finally, it is shown that if the mean flow in computing the transmission loss of the mufflers involving hyperbolic and parabolic shapes was not neglected, little practical benefit would be derived.

The generalized Onsager model for the secondary flow in a high-speed rotating cylinder

The generalizations of the Onsager model for the radial boundary layer and the Carrier-Maslen model for the end-cap axial boundary layer in a high-speed rotating cylinder are formulated for studying the secondary gas flow due to wall heating and due to insertion of mass, momentum and energy into the cylinder. The generalizations have wider applicability than the original Onsager and Carrier-Maslen models, because they are not restricted to the limit A >> 1, though they are restricted to the limit R e >> 1 and a high-aspect-ratio cylinder whose length/diameter ratio is large. Here, the stratification parameter A = root m Omega(2)R(2)/2k(B)T). This parameter A is the ratio of the peripheral speed, Omega R, to the most probable molecular speed, root 2k(B)T/m, the Reynolds number Re = rho w Omega R(2)/mu, where m is the molecular mass, Omega and R are the rotational speed and radius of the cylinder, k(B) is the Boltzmann constant, T is the gas temperature, rho(w) is the gas density at wall, and mu is the gas viscosity. In the case of wall forcing, analytical solutions are obtained for the sixth-order generalized Onsager equations for the master potential, and for the fourth-order generalized Carrier-Maslen equation for the velocity potential. For the case of mass/momentum/energy insertion into the flow, the separation-of-variables procedure is used, and the appropriate homogeneous boundary conditions are specified so that the linear operators in the axial and radial directions are self-adjoint. The discrete eigenvalues and eigenfunctions of the linear operators (sixth-order and second-order in the radial and axial directions for the Onsager equation, and fourth-order and second-order in the axial and radial directions for the Carrier-Maslen equation) are determined. These solutions are compared with direct simulation Monte Carlo (DSMC) simulations. The comparison reveals that the boundary conditions in the simulations and analysis have to be matched with care. The commonly used `diffuse reflection' boundary conditions at solid walls in DSMC simulations result in a non-zero slip velocity as well as a `temperature slip' (gas temperature at the wall is different from wall temperature). These have to be incorporated in the analysis in order to make quantitative predictions. In the case of mass/momentum/energy sources within the flow, it is necessary to ensure that the homogeneous boundary conditions are accurately satisfied in the simulations. When these precautions are taken, there is excellent agreement between analysis and simulations, to within 10 %, even when the stratification parameter is as low as 0.707, the Reynolds number is as low as 100 and the aspect ratio (length/diameter) of the cylinder is as low as 2, and the secondary flow velocity is as high as 0.2 times the maximum base flow velocity. The predictions of the generalized models are also significantly better than those of the original Onsager and Carrier-Maslen models, which are restricted to thin boundary layers in the limit of high stratification parameter.

Kinetics and chemical analysis of photoinduced interdiffusion in nanolayered Se/As2S3 films

We have studied the kinetics of photoinduced effects in nanolayered Se/As2S3 film by in situ optical absorption measurements, which reveal that photodarkening in these films is followed by photoinduced diffusion. An increase in disorder during photodarkening and its subsequent decrease during photoinduced diffusion were also observed. The observation of photodarkening of Se at room temperature when confined between As2S3 layers suggests that the glass transition temperature of Se shifts to higher energy. The analysis shows that the atoms which take part in photodarkening play a vital role in photoinduced diffusion. The x-ray photoelectron spectroscopy measurements show the atomic movements during photoinduced diffusion. It also shows that some of the As–S bonds are converted into As–Se bonds. Since it is energetically difficult to break an As–S bond to form an As–Se bond, we assume that the new bond formations are taking place by the bond rearrangement mechanism.

Particle dynamics in the channel flow of a turbulent particle-gas suspension at high Stokes number. Part 1. DNS and fluctuating force model

The fluctuating force model is developed and applied to the turbulent flow of a gas-particle suspension in a channel in the limit of high Stokes number, where the particle relaxation time is large compared to the fluid correlation time, and low particle Reynolds number where the Stokes drag law can be used to describe the interaction between the particles and fluid. In contrast to the Couette flow, the fluid velocity variances in the different directions in the channel are highly non-homogeneous, and they exhibit significant variation across the channel. First, we analyse the fluctuating particle velocity and acceleration distributions at different locations across the channel. The distributions are found to be non-Gaussian near the centre of the channel, and they exhibit significant skewness and flatness. However, acceleration distributions are closer to Gaussian at locations away from the channel centre, especially in regions where the variances of the fluid velocity fluctuations are at a maximum. The time correlations for the fluid velocity fluctuations and particle acceleration fluctuations are evaluated, and it is found that the time correlation of the particle acceleration fluctuations is close to the time correlations of the fluid velocity in a `moving Eulerian' reference, moving with the mean fluid velocity. The variances of the fluctuating force distributions in the Langevin simulations are determined from the time correlations of the fluid velocity fluctuations and the results are compared with direct numerical simulations. Quantitative agreement between the two simulations are obtained provided the particle viscous relaxation time is at least five times larger than the fluid integral time.

Particle dynamics in the channel flow of a turbulent particle-gas suspension at high Stokes number. Part 2. Comparison of fluctuating force simulations and experiments

The particle and fluid velocity fluctuations in a turbulent gas-particle suspension are studied experimentally using two-dimensional particle image velocimetry with the objective of comparing the experiments with the predictions of fluctuating force simulations. Since the fluctuating force simulations employ force distributions which do not incorporate the modification of fluid turbulence due to the particles, it is of importance to quantify the turbulence modification in the experiments. For experiments carried out at a low volume fraction of 9.15 x 10(-5) (mass loading is 0.19), where the viscous relaxation time is small compared with the time between collisions, it is found that the gas-phase turbulence is not significantly modified by the presence of particles. Owing to this, quantitative agreement is obtained between the results of experiments and fluctuating force simulations for the mean velocity and the root mean square of the fluctuating velocity, provided that the polydispersity in the particle size is incorporated in the simulations. This is because the polydispersity results in a variation in the terminal velocity of the particles which could induce collisions and generate fluctuations; this mechanism is absent if all of the particles are of equal size. It is found that there is some variation in the particle mean velocity very close to the wall depending on the wall-collision model used in the simulations, and agreement with experiments is obtained only when the tangential wall-particle coefficient of restitution is 0.7. The mean particle velocity is in quantitative agreement for locations more than 10 wall units from the wall of the channel. However, there are systematic differences between the simulations and theory for the particle concentrations, possibly due to inadequate control over the particle feeding at the entrance. The particle velocity distributions are compared both at the centre of the channel and near the wall, and the shape of the distribution function near the wall obtained in experiments is accurately predicted by the simulations. At the centre, there is some discrepancy between simulations and experiment for the distribution of the fluctuating velocity in the flow direction, where the simulations predict a bi-modal distribution whereas only a single maximum is observed in the experiments, although both distributions are skewed towards negative fluctuating velocities. At a much higher particle mass loading of 1.7, where the time between collisions is smaller than the viscous relaxation time, there is a significant increase in the turbulent velocity fluctuations by similar to 1-2 orders of magnitude. Therefore, it becomes necessary to incorporate the modified fluid-phase intensity in the fluctuating force simulation; with this modification, the mean and mean-square fluctuating velocities are within 20-30% of the experimental values.

Flow-acoustic Characterisation of a Cavity-based Combustor Configuration

This study concerns the flow-acoustic characterisation of a cavity-based combustor configuration. A well-validated numerical tool has been used to simulate the unsteady, two-dimensional reacting flow. Initially, a conventional flow over a cavity with dimensions and conditions corresponding to a compact cavity combustor was studied. Cavity mass injections in the form of fuel and air injections required for trapped vortex formation were then employed and the resonance features of this configuration were studied. The results indicate that the cavity depth mode resonance mechanism is dominant at the conditions studied in this work and that the oscillation frequencies do not change with cavity air injection. This observation is important since it implies that the only important variable which can alter resonant frequencies is the cavity depth. With combustion, the pressure oscillation amplitude was observed to increases significantly due to periodic entrainment of the cavity air jet and fluctuation of fuel-air mixture composition to produce highly fluctuating heat-release rates. The underlying mechanisms of the unsteady flow in the cavity combustor identified in this study indicate the strong dependence of the acoustics on the cavity injection strategies.

On the mechanism of plastic flow at 86°k in quenched and aged aluminum

The plastic flow of quenched aluminium at 86°K was investigated by ‘differential-stress’ creep tests in order to evaluate the rate-controlling mechanism in as-quenched and fully aged states. The experimental values of activation volume (4·3 × 10−21 cm3 for as-quenched and 5·5×l0−21cm3 for fully aged) and the total energy for thermal activation process (0·4 ev for both) are in accordance with the jog hardening and loop hardening mechanisms in quenched and fully aged states respectively.

Dislocation mechanisms for plastic flow of nickel in the temperature range 4.2 – 1200 K

The temperature ranges of thermal and athermal deformation behaviour of nickel are identified by employing the temperature-dependence of flow-stress and strain-rate cycling data. The results are used to present a unified view of dislocation mechanisms of glide encompassing the two thermally activated and the intermediate athermal regimes of plastic flow.In the low-temperature thermally activated region (<250 K) the strain rate is found to be controlled by the repulsive intersection of glide and forest dislocations, in accordance with current ideas. The athermal stress in this region can be attributed mainly to the presence of strong attractive junctions which are overcome by means of Orowan bowing, a small contribution also coming from the elastic interactions between dislocations. The values of activation area and activation energy obtained in the high-temperature region (> 750 K) negate the operation of a diffusion-controlled mechanism. Instead, the data support a thermal activation model involving unzipping of the attractive junctions. The internal (long-range) stress contribution here results solely from the elastic interactions between dislocations. This view concerning the high-temperature plastic flow is further supported by the observation that the Cottrell–Stokes law is obeyed over large strains in the range 750–1200 K.

Mathematical Model of Viral Kinetics In Vitro Estimates the Number of E2-CD81 Complexes Necessary for Hepatitis C Virus Entry

Interaction between the hepatitis C virus (HCV) envelope protein E2 and the host receptor CD81 is essential for HCV entry into target cells. The number of E2-CD81 complexes necessary for HCV entry has remained difficult to estimate experimentally. Using the recently developed cell culture systems that allow persistent HCV infection in vitro, the dependence of HCV entry and kinetics on CD81 expression has been measured. We reasoned that analysis of the latter experiments using a mathematical model of viral kinetics may yield estimates of the number of E2-CD81 complexes necessary for HCV entry. Here, we constructed a mathematical model of HCV viral kinetics in vitro, in which we accounted explicitly for the dependence of HCV entry on CD81 expression. Model predictions of viral kinetics are in quantitative agreement with experimental observations. Specifically, our model predicts triphasic viral kinetics in vitro, where the first phase is characterized by cell proliferation, the second by the infection of susceptible cells and the third by the growth of cells refractory to infection. By fitting model predictions to the above data, we were able to estimate the threshold number of E2-CD81 complexes necessary for HCV entry into human hepatoma-derived cells. We found that depending on the E2-CD81 binding affinity, between 1 and 13 E2-CD81 complexes are necessary for HCV entry. With this estimate, our model captured data from independent experiments that employed different HCV clones and cells with distinct CD81 expression levels, indicating that the estimate is robust. Our study thus quantifies the molecular requirements of HCV entry and suggests guidelines for intervention strategies that target the E2-CD81 interaction. Further, our model presents a framework for quantitative analyses of cell culture studies now extensively employed to investigate HCV infection.

Kinetics of carbon monoxide oxidation with Sn(0.95)M(0.05)O(2-delta) (M = Cu, Fe, Mn, Co) catalysts

Base metal substituted Sn(0.95)M(0.05)O(2-delta) (M = Cu, Fe, Mn, Co) catalysts were synthesized by the solution combustion method and characterized by XRD, XPS, TEM and BET surface area analysis. The catalytic activities of these materials were investigated by performing CO oxidation. The rates and the apparent activation energies of the reaction for CO oxidation were determined for each catalyst. All the substituted catalysts showed high rates and lower activation energies for the oxidation of CO as compared to unsubstituted SnO(2). The rate was found to be much higher over copper substituted SnO(2) as compared to other studied catalysts. 100% CO conversion was obtained below 225 degrees C over this catalyst. A bifunctional reaction mechanism was developed that accounts for CO adsorption on base metal and support ions and O(2) dissociation on the oxide ion vacancy. The kinetic parameters were determined by fitting the model to the experimental data. The high rates of the CO oxidation reactions at low temperatures were rationalized by the high dissociative chemisorption of adsorbed O(2) over these catalysts.

Effects of acoustic-streaming-induced flow in evaporating nanofluid droplets

We study the effect of acoustic streaming on nanoparticle motion and morphological evolution inside an acoustically levitated droplet using an analytical approach coupled with experiments. Nanoparticle migration due to internal recirculation forms a density stratification, the location of which depends on initial particle concentration. The time scale of density stratification is similar to that of perikinetic-driven agglomeration of particle flocculation. The density stratification ultimately leads to force imbalance leading to a unique bowl-shaped structure. Our analysis shows the mechanism of bowl formation and how it is affected by particle size, concentration, internal recirculation and fluid viscosity.

Differential Reaction Kinetics, Cleavage Complex Formation, and Nonamer Binding Domain Dependence Dictate the Structure-Specific and Sequence-Specific Nuclease Activity of RAGs

During V(D)J recombination, RAG (recombination-activating gene) complex cleaves DNA based on sequence specificity. Besides its physiological function, RAG has been shown to act as a structure-specific nuclease. Recently, we showed that the presence of cytosine within the single-stranded region of heteroduplex DNA is important when RAGs cleave on DNA structures. In the present study, we report that heteroduplex DNA containing a bubble region can be cleaved efficiently when present along with a recombination signal sequence (RSS) in cis or trans configuration. The sequence of the bubble region influences RAG cleavage at RSS when present in cis. We also find that the kinetics of RAG cleavage differs between RSS and bubble, wherein RSS cleavage reaches maximum efficiency faster than bubble cleavage. In addition, unlike RSS, RAG cleavage at bubbles does not lead to cleavage complex formation. Finally, we show that the ``nonamer binding region,'' which regulates RAG cleavage on RSS, is not important during RAG activity in non-B DNA structures. Therefore, in the current study, we identify the possible mechanism by which RAG cleavage is regulated when it acts as a structure-specific nuclease. (C) 2011 Elsevier Ltd. All rights reserved.

Surface pressure and heat transfer measurements in the unsteady separated hypersonic flow field over double cones

Reliable bench mark experimental database in the separated hypersonic flow regime is necessary to validate high resolution CFD codes. In this paper we report the surface pressure and heat transfer measurements carried out on double cones (first cone semi-apex angle = 15, 25 deg.; second cone semi-apex angle= 35, 68 deg.) at hypersonic speeds that will be useful for CFD code validation studies. The surface pressure measurements are carried out at nominal Mach number of 8.35 in the IISc hypersonic wind tunnel. On the other hand the surface heat transfer measurements are carried out at a nominal Mach number of 5.75 in the IISc hypersonic shock tunnel. The flow separation point on the first cone, flow reattachment on the second cone and the wild fluctuation of the transmitted shock on the second cone surface (25/68 deg. double cone) in the presence of severe adverse pressure gradient are some of the flow features captured in the measurements. The results from the CFD studies indicate good agreement with experiments in the attached flow regime while considerable differences are noticeable in the separated flow regime.