Exact solution at integrable coupling of a model for the Josephson effect between small metallic grains

A model is introduced for two reduced BCS systems which are coupled through the transfer of Cooper pairs between the systems. The model may thus be used in the analysis of the Josephson effect arising from pair tunneling between two strongly coupled small metallic grains. At a particular coupling strength the model is integrable and explicit results are derived for the energy spectrum, conserved operators, integrals of motion, and wave function scalar products. It is also shown that form factors can be obtained for the calculation of correlation functions. Furthermore, a connection with perturbed conformal field theory is made.

A model of factors affecting an information system's change in state

Management are keen to maximize the life span of an information system because of the high cost, organizational disruption, and risk of failure associated with the re-development or replacement of an information system. This research investigates the effects that various factors have on an information system's life span by understanding how the factors affect an information system's stability. The research builds on a previously developed two-stage model of information system change whereby an information system is either in a stable state of evolution in which the information system's functionality is evolving, or in a state of revolution, in which the information system is being replaced because it is not providing the functionality expected by its users. A case study surveyed a number of systems within one organization. The aim was to test whether a relationship existed between the base value of the volatility index (a measure of the stability of an information system) and certain system characteristics. Data relating to some 3000 user change requests covering 40 systems over a 10-year period were obtained. The following factors were hypothesized to have significant associations with the base value of the volatility index: language level (generation of language of construction), system size, system age, and the timing of changes applied to a system. Significant associations were found in the hypothesized directions except that the timing of user changes was not associated with any change in the value of the volatility index. Copyright (C) 2002 John Wiley Sons, Ltd.

The damped and coherently-driven Jaynes-Cummings model

We investigate the influence of a single-mode cavity on the Autler-Townes doublet that arises when a three-level atom is strongly driven by a laser field tuned to one of the atomic transitions and probed by a tunable, weak field coupled to the other transition. We assume that the cavity mode is coupled to the driven transition and the cavity and laser frequencies are equal to the atomic transition frequency. We find that the Autler-Townes spectrum can have one, two or three peaks depending on the relative magnitudes of the Rabi frequencies of the cavity and driving fields. We show that, in order to understand the three-peaked spectrum, it is necessary to go beyond the secular approximation, leading to interesting quantum interference effects. We find that the positions and relative intensities of the three spectral components are affected strongly by the atom-cavity coupling strength g and the cavity damping K. For an increasing g and/or decreasing K the triplet evolves into a single peak. This results in 'undressing' of the system such that the atom collapses into its ground state. We interpret the spectral features in terms of the semiclassical dressed-atom model, and also provide complementary views of the cavity effects in terms of quantum Langevin equations and the fully quantized, 'double -dressing' model.

Assessment of the ability to model proteins with leucine-rich repeats in light of the latest structural information

The three-dimensional structures of leucine-rich repeat (LRR) -containing proteins from five different families were previously predicted based on the crystal structure of the ribonuclease inhibitor. using an approach that combined homology-based modeling, structure-based sequence alignment of LRRs, and several rational assumptions. The structural models have been produced based on very limited sequence similarity, which, in general. cannot yield trustworthy predictions. Recently, the protein structures from three of these five families have been determined. In this report we estimate the quality of the modeling approach by comparing the models with the experimentally determined structures. The comparison suggests that the general architecture, curvature, interior/exterior orientations of side chains. and backbone conformation of the LRR structures can be predicted correctly. On the other hand. the analysis revealed that, in some cases. it is difficult to predict correctly the twist of the overall super-helical structure. Taking into consideration the conclusions from these comparisons, we identified a new family of bacterial LRR proteins and present its structural model. The reliability of the LRR protein modeling suggests that it would be informative to apply similar modeling approaches to other classes of solenoid proteins.

Simulation of Oxford University Gun Tunnel performance using a quasi-one-dimensional model

The performance of the Oxford University Gun Tunnel has been estimated using a quasi-one-dimensional simulation of the facility gas dynamics. The modelling of the actual facility area variations so as to adequately simulate both shock reflection and flow discharge processes has been considered in some detail. Test gas stagnation pressure and temperature histories are compared with measurements at two different operating conditions - one with nitrogen and the other with carbon dioxide as the test gas. It is demonstrated that both the simulated pressures and temperatures are typically within 3% of the experimental measurements.

Monitoring the composition and form of urban environments based on the vegetation-impervious surface-soil (VIS) model by sub-pixel analysis techniques

The majority of the world's population now resides in urban environments and information on the internal composition and dynamics of these environments is essential to enable preservation of certain standards of living. Remotely sensed data, especially the global coverage of moderate spatial resolution satellites such as Landsat, Indian Resource Satellite and Systeme Pour I'Observation de la Terre (SPOT), offer a highly useful data source for mapping the composition of these cities and examining their changes over time. The utility and range of applications for remotely sensed data in urban environments could be improved with a more appropriate conceptual model relating urban environments to the sampling resolutions of imaging sensors and processing routines. Hence, the aim of this work was to take the Vegetation-Impervious surface-Soil (VIS) model of urban composition and match it with the most appropriate image processing methodology to deliver information on VIS composition for urban environments. Several approaches were evaluated for mapping the urban composition of Brisbane city (south-cast Queensland, Australia) using Landsat 5 Thematic Mapper data and 1:5000 aerial photographs. The methods evaluated were: image classification; interpretation of aerial photographs; and constrained linear mixture analysis. Over 900 reference sample points on four transects were extracted from the aerial photographs and used as a basis to check output of the classification and mixture analysis. Distinctive zonations of VIS related to urban composition were found in the per-pixel classification and aggregated air-photo interpretation; however, significant spectral confusion also resulted between classes. In contrast, the VIS fraction images produced from the mixture analysis enabled distinctive densities of commercial, industrial and residential zones within the city to be clearly defined, based on their relative amount of vegetation cover. The soil fraction image served as an index for areas being (re)developed. The logical match of a low (L)-resolution, spectral mixture analysis approach with the moderate spatial resolution image data, ensured the processing model matched the spectrally heterogeneous nature of the urban environments at the scale of Landsat Thematic Mapper data.

Mapping Gray's model of personality onto the Eysenck Personality Profiler (EPP)

The aim of this study was to determine how well Gray's model of personality [Gray, J.A. (1982). The neuropsychology of anxiety: an enquiry into the functions of the septo-hippocampal system. Oxfords: Oxford University Press, Gray, J.A. (1987). The psychology of fear and stress. Cambridge: Cambridge University Press], as measured by the Gray Wilson Personality Questionnaire (GWPQ), can provide a full description of personality as measured by the primary scales of the Eysenck Personality Profiler (EPP) and the type scales of the short version or the EPQ-R. Factor analysis of the GWPQ the Anxiety and linpulsivity scales of the EPP and the Learning Styles Questionnaire (LSQ) showed that the GWPQ seemed to measure general activation and inhibition factors, but not the finer features of Gray's theory. When the GWPQ scales were regressed against each scale of the EPP., it was round that they generally provide only a reasonable explanation of the EPP primary scales. It is concluded that the GWPQ measures general propel-ties of Gray's model, that the linpulsivity and Anxiety scales of the EPP also scent related to the GWPQ scales, and that Gray's model of personality provides only a partial explanation of personality in general. (C) 2002 Published by Elsevier Science Ltd. All rights reserved.

Structural ordering of coal char during heat treatment and its impact on reactivity

The effect of heat treatment on the structure of an Australian semi-anthracite char was studied in detail in the 850-1150degreesC temperature range using XRD, HRTEM, and electrical resistivity techniques. It was found that the carbon crystallite size in the char does not change significantly during heat treatment in the temperature range studied, for both the raw coal and its ash-free derivative obtained by acid treatment. However, the fraction of the organized carbon in the raw coal chars, determined by XRD, increased with increase of heat treatment time and temperature, while that for the ash-free coal chars remained almost unchanged. This suggests the occurrence of catalytic ordering during heat treatment, supported by the observation that the electrical resistivity of the raw coal chars decreased with heat treatment, while that of the ash-free coal chars did not vary significantly. Further confirmatory evidence was provided by high resolution transmission electron micrographs depicting well-organized carbon layers surrounding iron particles. It is also found that the fraction of organized carbon does not reach unity, but attains an apparent equilibrium value that increases with increase in temperature, providing an apparent heat of ordering of 71.7 kJ mol(-1) in the temperature range studied. Good temperature-independent correlation was found between the electrical resistivity and the organized carbon fraction, indicating that electrical resistivity is indeed structure sensitive. Good correlation was also found between the electrical resistivity and the reactivity of coal char. All these results strongly suggest that the thermal deactivation is the result of a crystallite-perfecting process, which is effectively catalyzed by the inorganic matter in the coal char. Based on kinetic interpretation of the data it is concluded that the process is diffusion controlled, most likely involving transport of iron in the inter-crystallite nanospaces in the temperature range studied. The activation energy of this transport process is found to be very low, at about 11.8 kJ mol(-1), which is corroborated by model-free correlation of the temporal variation of organized carbon fraction as well as electrical resistivity data using the superposition method, and is suggestive of surface transport of iron. (C) 2002 Elsevier Science Ltd. All rights reserved.

Application of the maximum entropy method to the (2 + 1)D four-fermion model

We investigate spectral functions extracted using the maximum entropy method from correlators measured in lattice simulations of the (2+1)-dimensional four-fermion model. This model is particularly interesting because it has both a chirally broken phase with a rich spectrum of mesonic bound states and a symmetric phase where there are only resonances. In the broken phase we study the elementary fermion, pion, sigma, and massive pseudoscalar meson; our results confirm the Goldstone nature of the π and permit an estimate of the meson binding energy. We have, however, seen no signal of σ→ππ decay as the chiral limit is approached. In the symmetric phase we observe a resonance of nonzero width in qualitative agreement with analytic expectations; in addition the ultraviolet behavior of the spectral functions is consistent with the large nonperturbative anomalous dimension for fermion composite operators expected in this model.

Development of a generic crop model template in the cropping system model APSIM

The Agricultural Production Systems slMulator, APSIM, is a cropping system modelling environment that simulates the dynamics of soil-plant-management interactions within a single crop or a cropping system. Adaptation of previously developed crop models has resulted in multiple crop modules in APSIM, which have low scientific transparency and code efficiency. A generic crop model template (GCROP) has been developed to capture unifying physiological principles across crops (plant types) and to provide modular and efficient code for crop modelling. It comprises a standard crop interface to the APSIM engine, a generic crop model structure, a crop process library, and well-structured crop parameter files. The process library contains the major science underpinning the crop models and incorporates generic routines based on physiological principles for growth and development processes that are common across crops. It allows APSIM to simulate different crops using the same set of computer code. The generic model structure and parameter files provide an easy way to test, modify, exchange and compare modelling approaches at process level without necessitating changes in the code. The standard interface generalises the model inputs and outputs, and utilises a standard protocol to communicate with other APSIM modules through the APSIM engine. The crop template serves as a convenient means to test new insights and compare approaches to component modelling, while maintaining a focus on predictive capability. This paper describes and discusses the scientific basis, the design, implementation and future development of the crop template in APSIM. On this basis, we argue that the combination of good software engineering with sound crop science can enhance the rate of advance in crop modelling. Crown Copyright (C) 2002 Published by Elsevier Science B.V. All rights reserved.

Polyethylene flow prediction with a differential multi-mode Pom-Pom model

We report the first steps of a collaborative project between the University of Queensland, Polyflow, Michelin, SK Chemicals, and RMIT University; on simulation, validation and application of a recently introduced constitutive model designed to describe branched polymers. Whereas much progress has been made on predicting the complex flow behaviour of many - in particular linear - polymers, it sometimes appears difficult to predict simultaneously shear thinning and extensional strain hardening behaviour using traditional constitutive models. Recently a new viscoelastic model based on molecular topology, was proposed by McLeish and Larson (1998). We explore the predictive power of a differential multi-mode version of the pom-pom model for the flow behaviour of two commercial polymer melts: a (long-chain branched) low-density polyethylene (LDPE) and a (linear) high-density polyethylene (HDPE). The model responses are compared to elongational recovery experiments published by Langouche and Debbaut (1999), and start-up of simple shear flow, stress relaxation after simple and reverse step strain experiments carried out in our laboratory.

Finite difference time domain (FDTD) method for modeling the effect of switched gradients on the human body in MRI

Numerical modeling of the eddy currents induced in the human body by the pulsed field gradients in MRI presents a difficult computational problem. It requires an efficient and accurate computational method for high spatial resolution analyses with a relatively low input frequency. In this article, a new technique is described which allows the finite difference time domain (FDTD) method to be efficiently applied over a very large frequency range, including low frequencies. This is not the case in conventional FDTD-based methods. A method of implementing streamline gradients in FDTD is presented, as well as comparative analyses which show that the correct source injection in the FDTD simulation plays a crucial rule in obtaining accurate solutions. In particular, making use of the derivative of the input source waveform is shown to provide distinct benefits in accuracy over direct source injection. In the method, no alterations to the properties of either the source or the transmission media are required. The method is essentially frequency independent and the source injection method has been verified against examples with analytical solutions. Results are presented showing the spatial distribution of gradient-induced electric fields and eddy currents in a complete body model.

Cyclosporin A pretreatment in a rat model of warm ischaemia/reperfusion injury

Background/Aims: These studies investigated the role of apoptosis following ischaemia/reperfusion (I/R) injury to the liver and the effect of pretreatment with Cyclosporin A. Methods: Male Sprague-Dawley rats received 30 min of warm ischaemia followed by a period of reperfusion of 6 h. Rats were given olive oil or Cyclosporin A (30 mg/kg p.o.) the day before surgery. Neutrophil numbers were assessed in haematoxylin-eosin-stained sections of liver. In situ staining of sections using TdT-mediated dUTP-fluoreseein nick-end labelling was carried out to determine the extent of apoptosis, followed by electron microscopy. Semi-quantitative polymerase chain reaction (PCR) analysis of the transcript for Fas antigen was performed. Results and Conclusions: High levels of apoptosis were observed in I/R injury, which were greatly ameliorated in Cyclosporin A-pretreated groups. PCR analysis indicated a reduction in the level of expression of Fas transcript in Cyclosporin A-treated rats. Histological analysis showed a significant increase in the number of neutrophils infiltrating I/R-injured tissue (62 +/- 10.69, it = 16), which was markedly reduced by Cyclosporin A pretreatment (16 +/- 7, n = 6, P < 0.05). These results indicate a role of parenchymal apoptosis in the pathogenesis of I/R injury, which occurs in association with neutrophil infiltration, both of which can be significantly reduced by Cyclosporin A pretreatment. (C) 2002 European Association for the Study of the Liver. Published by Elsevier Science B.V. All rights reserved.

The E(NK) model: extending the NK model to incorporate gene-by-environment interactions and epistasis for diploid genomes

The haploid NK model developed by Kauffman can be extended to diploid genomes and to incorporate gene-by-environment interaction effects in combination with epistasis. To provide the flexibility to include a wide range of forms of gene-by-environment interactions, a target population of environment types (TPE) is defined. The TPE consists of a set of E different environment types, each with their own frequency of occurrence. Each environment type conditions a different NK gene network structure or series of gene effects for a given network structure, providing the framework for defining gene-by-environment interactions. Thus, different NK models can be partially or completely nested within the E environment types of a TPE, giving rise to the E(NK) model for a biological system. With this model it is possible to examine how populations of genotypes evolve in context with properties of the environment that influence the contributions of genes to the fitness values of genotypes. We are using the E(NK) model to investigate how both epistasis and gene-by-environment interactions influence the genetic improvement of quantitative traits by plant breeding strategies applied to agricultural systems. © 2002 Wiley Periodicals, Inc.

The GP problem: quantifying gene-to-phenotype relationships

In this paper we refer to the gene-to-phenotype modeling challenge as the GP problem. Integrating information across levels of organization within a genotype-environment system is a major challenge in computational biology. However, resolving the GP problem is a fundamental requirement if we are to understand and predict phenotypes given knowledge of the genome and model dynamic properties of biological systems. Organisms are consequences of this integration, and it is a major property of biological systems that underlies the responses we observe. We discuss the E(NK) model as a framework for investigation of the GP problem and the prediction of system properties at different levels of organization. We apply this quantitative framework to an investigation of the processes involved in genetic improvement of plants for agriculture. In our analysis, N genes determine the genetic variation for a set of traits that are responsible for plant adaptation to E environment-types within a target population of environments. The N genes can interact in epistatic NK gene-networks through the way that they influence plant growth and development processes within a dynamic crop growth model. We use a sorghum crop growth model, available within the APSIM agricultural production systems simulation model, to integrate the gene-environment interactions that occur during growth and development and to predict genotype-to-phenotype relationships for a given E(NK) model. Directional selection is then applied to the population of genotypes, based on their predicted phenotypes, to simulate the dynamic aspects of genetic improvement by a plant-breeding program. The outcomes of the simulated breeding are evaluated across cycles of selection in terms of the changes in allele frequencies for the N genes and the genotypic and phenotypic values of the populations of genotypes.