The Equilibrium Flux Method for the calculation of flows with non-equilbrium chemical reactions

The Equilibrium Flux Method [1] is a kinetic theory based finite volume method for calculating the flow of a compressible ideal gas. It is shown here that, in effect, the method solves the Euler equations with added pseudo-dissipative terms and that it is a natural upwinding scheme. The method can be easily modified so that the flow of a chemically reacting gas mixture can be calculated. Results from the method for a one-dimensional non-equilibrium reacting flow are shown to agree well with a conventional continuum solution. Results are also presented for the calculation of a plane two-dimensional flow, at hypersonic speed, of a dissociating gas around a blunt-nosed body.

Towards realistic simulations of lava dome growth using the level set method

The level set method has been implemented in a computational volcanology context. New techniques are presented to solve the advection equation and the reinitialisation equation. These techniques are based upon an algorithm developed in the finite difference context, but are modified to take advantage of the robustness of the finite element method. The resulting algorithm is tested on a well documented Rayleigh–Taylor instability benchmark [19], and on an axisymmetric problem where the analytical solution is known. Finally, the algorithm is applied to a basic study of lava dome growth.

A method to lower the detection limit for optical beat signals from a frequency-dithered stabilized laser

A narrow absorption feature in an atomic or molecular gas (such as iodine or methane) is used as the frequency reference in many stabilized lasers. As part of the stabilization scheme an optical frequency dither is applied to the laser. In optical heterodyne experiments, this dither is transferred to the RF beat signal, reducing the spectral power density and hence the signal to noise ratio over that in the absence of dither. We removed the dither by mixing the raw beat signal with a dithered local oscillator signal. When the dither waveform is matched to that of the reference laser the output signal from the mixer is rendered dither free. Application of this method to a Winters iodine-stabilized helium-neon laser reduced the bandwidth of the beat signal from 6 MHz to 390 kHz, thereby lowering the detection threshold from 5 pW of laser power to 3 pW. In addition, a simple signal detection model is developed which predicts similar threshold reductions.

Wolbachia pipientis: bacterial density and unidirectional cytoplasmic incompatibility between infected populations of Aedes albopictus

Unidirectional cytoplasmic incompatibility is seen when certain Wolbachia-infected insect populations are crossed. Two hypotheses might explain this phenomenon: superinfections with mutually incompatible strains of Wolbachia producing incompatibility when crossed to individuals infected with only a single bacterial strain or, alternatively, a bacterial dosage model, with differences in Wolbachia densities responsible for the incompatibility. A quantitative PCR assay was set up as a general method to compare Wolbachia densities between populations. Using this assay in unidirectionally incompatible stocks of the mosquito Aedes albopictus, we have determined that densities are significantly higher in Houston than in the Mauritius and Koh Samui stocks. This is consistent with a dosage model for the observed crossing patterns, but does not rule out the possibility that superinfection is the primary cause of the incompatibility.

Clifford Geertz, 1926-2006: Meaning, method, and Indonesian economic history

Clifford Geertz was best known for his pioneering excursions into symbolic or interpretive anthropology, especially in relation to Indonesia. Less well recognised are his stimulating explorations of the modern economic history of Indonesia. His thinking on the interplay of economics and culture was most fully and vigorously expounded in Agricultural Involution. That book deployed a succinctly packaged past in order to solve a pressing contemporary puzzle, Java's enduring rural poverty and apparent social immobility. Initially greeted with acclaim, later and ironically the book stimulated the deep and multi-layered research that in fact led to the eventual rejection of Geertz's central contentions. But the veracity or otherwise of Geertz's inventive characterisation of Indonesian economic development now seems irrelevant; what is profoundly important is the extraordinary stimulus he gave to a generation of scholars to explore Indonesia's modern economic history with a depth and intensity previously unimaginable.

Algebraic Bethe ansatz method for the exact calculation of energy spectra and form factors: applications to models of Bose-Einstein condensates and metallic nanograins

In this review we demonstrate how the algebraic Bethe ansatz is used for the calculation of the-energy spectra and form factors (operator matrix elements in the basis of Hamiltonian eigenstates) in exactly solvable quantum systems. As examples we apply the theory to several models of current interest in the study of Bose-Einstein condensates, which have been successfully created using ultracold dilute atomic gases. The first model we introduce describes Josephson tunnelling between two coupled Bose-Einstein condensates. It can be used not only for the study of tunnelling between condensates of atomic gases, but for solid state Josephson junctions and coupled Cooper pair boxes. The theory is also applicable to models of atomic-molecular Bose-Einstein condensates, with two examples given and analysed. Additionally, these same two models are relevant to studies in quantum optics; Finally, we discuss the model of Bardeen, Cooper and Schrieffer in this framework, which is appropriate for systems of ultracold fermionic atomic gases, as well as being applicable for the description of superconducting correlations in metallic grains with nanoscale dimensions.; In applying all the above models to. physical situations, the need for an exact analysis of small-scale systems is established due to large quantum fluctuations which render mean-field approaches inaccurate.

A fast cross-entropy method for estimating buffer overflows in queuing networks

In this paper, we propose a fast adaptive importance sampling method for the efficient simulation of buffer overflow probabilities in queueing networks. The method comprises three stages. First, we estimate the minimum cross-entropy tilting parameter for a small buffer level; next, we use this as a starting value for the estimation of the optimal tilting parameter for the actual (large) buffer level. Finally, the tilting parameter just found is used to estimate the overflow probability of interest. We study various properties of the method in more detail for the M/M/1 queue and conjecture that similar properties also hold for quite general queueing networks. Numerical results support this conjecture and demonstrate the high efficiency of the proposed algorithm.

An improved novel method for solving nonlinear boundary value problems

A modified formula for the integral transform of a nonlinear function is proposed for a class of nonlinear boundary value problems. The technique presented in this paper results in analytical solutions. Iterations and initial guess, which are needed in other techniques, are not required in this novel technique. The analytical solutions are found to agree surprisingly well with the numerically exact solutions for two examples of power law reaction and Langmuir-Hinshelwood reaction in a catalyst pellet.

Non-Equilibrium Reaction Rates in the Macroscopic Chemistry Method for DSMC Calculations

The Direct Simulation Monte Carlo (DSMC) method is used to simulate the flow of rarefied gases. In the Macroscopic Chemistry Method (MCM) for DSMC, chemical reaction rates calculated from local macroscopic flow properties are enforced in each cell. Unlike the standard total collision energy (TCE) chemistry model for DSMC, the new method is not restricted to an Arrhenius form of the reaction rate coefficient, nor is it restricted to a collision cross-section which yields a simple power-law viscosity. For reaction rates of interest in aerospace applications, chemically reacting collisions are generally infrequent events and, as such, local equilibrium conditions are established before a significant number of chemical reactions occur. Hence, the reaction rates which have been used in MCM have been calculated from the reaction rate data which are expected to be correct only for conditions of thermal equilibrium. Here we consider artificially high reaction rates so that the fraction of reacting collisions is not small and propose a simple method of estimating the rates of chemical reactions which can be used in the Macroscopic Chemistry Method in both equilibrium and non-equilibrium conditions. Two tests are presented: (1) The dissociation rates under conditions of thermal non-equilibrium are determined from a zero-dimensional Monte-Carlo sampling procedure which simulates ‘intra-modal’ non-equilibrium; that is, equilibrium distributions in each of the translational, rotational and vibrational modes but with different temperatures for each mode; (2) The 2-D hypersonic flow of molecular oxygen over a vertical plate at Mach 30 is calculated. In both cases the new method produces results in close agreement with those given by the standard TCE model in the same highly nonequilibrium conditions. We conclude that the general method of estimating the non-equilibrium reaction rate is a simple means by which information contained within non-equilibrium distribution functions predicted by the DSMC method can be included in the Macroscopic Chemistry Method.

A hybrid planning method for transmission networks in a deregulated environment

The reconstruction of power industries has brought fundamental changes to both power system operation and planning. This paper presents a new planning method using multi-objective optimization (MOOP) technique, as well as human knowledge, to expand the transmission network in open access schemes. The method starts with a candidate pool of feasible expansion plans. Consequent selection of the best candidates is carried out through a MOOP approach, of which multiple objectives are tackled simultaneously, aiming at integrating the market operation and planning as one unified process in context of deregulated system. Human knowledge has been applied in both stages to ensure the selection with practical engineering and management concerns. The expansion plan from MOOP is assessed by reliability criteria before it is finalized. The proposed method has been tested with the IEEE 14-bus system and relevant analyses and discussions have been presented.

Using the level set method to model endogenous lava dome growth

Modeling volcanic phenomena is complicated by free-surfaces often supporting large rheological gradients. Analytical solutions and analogue models provide explanations for fundamental characteristics of lava flows. But more sophisticated models are needed, incorporating improved physics and rheology to capture realistic events. To advance our understanding of the flow dynamics of highly viscous lava in Peléean lava dome formation, axi-symmetrical Finite Element Method (FEM) models of generic endogenous dome growth have been developed. We use a novel technique, the level-set method, which tracks a moving interface, leaving the mesh unaltered. The model equations are formulated in an Eulerian framework. In this paper we test the quality of this technique in our numerical scheme by considering existing analytical and experimental models of lava dome growth which assume a constant Newtonian viscosity. We then compare our model against analytical solutions for real lava domes extruded on Soufrière, St. Vincent, W.I. in 1979 and Mount St. Helens, USA in October 1980 using an effective viscosity. The level-set method is found to be computationally light and robust enough to model the free-surface of a growing lava dome. Also, by modeling the extruded lava with a constant pressure head this naturally results in a drop in extrusion rate with increasing dome height, which can explain lava dome growth observables more appropriately than when using a fixed extrusion rate. From the modeling point of view, the level-set method will ultimately provide an opportunity to capture more of the physics while benefiting from the numerical robustness of regular grids.

Specific PCR based detection of Phytophthora medicaginis using the intergenic spacer region of the ribosomal DNA

A technique based on the polymerase chain reaction (PCR) for the specific detection of Phytophthora medicaginis was developed using nucleotide sequence information of the ribosomal DNA (rDNA) regions. The complete IGS 2 region between the 5 S gene of one rDNA repeat and the small subunit of the adjacent repeat was sequenced for P. medicaginis and related species. The entire nucleotide sequence length of the IGS 2 of P. medicaginis was 3566 bp. A pair of oligonucleotide primers (PPED04 and PPED05), which allowed amplification of a specific fragment (364 bp) within the IGS 2 of P. medicaginis using the PCR, was designed. Specific amplification of this fragment from P. medicaginis was highly sensitive, detecting template DNA as low as 4 ng and in a host-pathogen DNA ratio of 1000000:1. Specific PCR amplification using PPED04 and PPED05 was successful in detecting P. medicaginis in lucerne stems infected under glasshouse conditions and field infected lucerne roots. The procedures developed in this work have application to improved identification and detection of a wide range of Phytophthora spp. in plants and soil.

Functional polymorphism of the human arylamine N-acetyltransferase type 1 gene caused by (CT)-T-190 and G(560)A mutations

Human N-acetyltransferase type 1 (NAT1) catalyses the N- or O-acetylation of various arylamine and heterocyclic amine substrates and is able to bioactivate several known carcinogens. Despite wide inter-individual variability in activity, historically, NAT1 was considered to be monomorphic in nature. However, recent reports of allelic variation at the NAT1 locus suggest that it may be a polymorphically expressed enzyme. In the present study, peripheral blood mononuclear cell NAT1 activity in 85 individuals was found to be bimodally distributed with approximately 8% of the population being slow acetylators. Subsequent sequencing of the individuals having slow acetylator status showed all to have either a (CT)-T-190 or G(560)A base substitution located in the protein encoding region of the NAT1 gene. The (CT)-T-190 base substitution changed a highly conserved Arg(64), which others have shown to be essential for fully functional NAT1 protein. The (CT)-T-190 mutation has not been reported previously and we have named it NAT1*17. The G(560)A mutation is associated with the base substitutions previously observed in the NAT1*10 allele and this variant (NAT1*14) encodes for a protein with reduced acetylation capacity. A novel method using linear PCR and dideoxy terminators was developed for the detection of NAT1*14 and NAT1*17. Neither of these variants was found in the rapid acetylator population. We conclude that both the (CT)-T-190 (NAT1*17) and G(560)A (NAT1*14) NAT1 structural variants are involved in a distinct NAT1 polymorphism. Because NAT1 can bioactivate several carcinogens, this polymorphism may have implications for cancer risk in individual subjects. (C) 1998 Chapman & Hall Ltd.