Modelling and simulation framework for reactive transport of organic contaminants in bed-sediments using a pure java object - oriented paradigm

Numerical modelling and simulation of organic contaminant reactive transport in the environment is being increasingly relied upon for a wide range of tasks associated with risk-based decision-making, such as prediction of contaminant profiles, optimisation of remediation methods, and monitoring of changes resulting from an implemented remediation scheme. The lack of integration of multiple mechanistic models to a single modelling framework, however, has prevented the field of reactive transport modelling in bed-sediments from developing a cohesive understanding of contaminant fate and behaviour in the aquatic sediment environment. This paper will investigate the problems involved in the model integration process, discuss modelling and software development approaches, and present preliminary results from use of CORETRANS, a predictive modelling framework that simulates 1-dimensional organic contaminant reaction and transport in bed-sediments

The DUNE-ALUGrid Module

In this paper we present the new DUNE-ALUGrid module. This module contains a major overhaul of the sources from the ALUgrid library and the binding to the DUNE software framework. The main changes include user defined load balancing, parallel grid construction, and an redesign of the 2d grid which can now also be used for parallel computations. In addition many improvements have been introduced into the code to increase the parallel efficiency and to decrease the memory footprint. The original ALUGrid library is widely used within the DUNE community due to its good parallel performance for problems requiring local adaptivity and dynamic load balancing. Therefore, this new model will benefit a number of DUNE users. In addition we have added features to increase the range of problems for which the grid manager can be used, for example, introducing a 3d tetrahedral grid using a parallel newest vertex bisection algorithm for conforming grid refinement. In this paper we will discuss the new features, extensions to the DUNE interface, and explain for various examples how the code is used in parallel environments.Comment: 25 pages, 11 figure

Multiport Impedance Quantization

With the increase of complexity and coherence of superconducting systems made using the principles of circuit quantum electrodynamics, more accurate methods are needed for the characterization, analysis and optimization of these quantum processors. Here we introduce a new method of modelling that can be applied to superconducting structures involving multiple Josephson junctions, high-Q superconducting cavities, external ports, and voltage sources. Our technique, an extension of our previous work on single-port structures [1], permits the derivation of system Hamiltonians that are capable of representing every feature of the physical system over a wide frequency band and the computation of T1 times for qubits. We begin with a black box model of the linear and passive part of the system. Its response is given by its multiport impedance function Zsim(w), which can be obtained using a finite-element electormagnetics simulator. The ports of this black box are defined by the terminal pairs of Josephson junctions, voltage sources, and 50 Ohm connectors to high-frequency lines. We fit Zsim(w) to a positive-real (PR) multiport impedance matrix Z(s), a function of the complex Laplace variable s. We then use state-space techniques to synthesize a finite electric circuit admitting exactly the same impedance Z(s) across its ports; the PR property ensures the existence of this finite physical circuit. We compare the performance of state-space algorithms to classical frequency domain methods, justifying their superiority in numerical stability. The Hamiltonian of the multiport model circuit is obtained by using existing lumped element circuit quantization formalisms [2, 3]. Due to the presence of ideal transformers in the model circuit, these quantization methods must be extended, requiring the introduction of an extension of the Kirchhoff voltage and current laws

Leveraging Semantic Web Service Descriptions for Validation by Automated Functional Testing

Recent years have seen the utilisation of Semantic Web Service descriptions for automating a wide range of service-related activities, with a primary focus on service discovery, composition, execution and mediation. An important area which so far has received less attention is service validation, whereby advertised services are proven to conform to required behavioural specifications. This paper proposes a method for validation of service-oriented systems through automated functional testing. The method leverages ontology-based and rule-based descriptions of service inputs, outputs, preconditions and effects (IOPE) for constructing a stateful EFSM specification. The specification is subsequently utilised for functional testing and validation using the proven Stream X-machine (SXM) testing methodology. Complete functional test sets are generated automatically at an abstract level and are then applied to concrete Web services, using test drivers created from the Web service descriptions. The testing method comes with completeness guarantees and provides a strong method for validating the behaviour of Web services

Biofilms in porous media: development of macroscopic transport equations via volume averaging with closure for local mass equilibrium conditions

In this work, we upscale a pore-scale description of mass transport in a porous medium containing biofilm to develop the relevant Darcy-scale equations. We begin with the pore-scale descriptions of mass transport, interphase mass transfer, and biologically-mediated reactions; these processes are then upscaled using the method of volume averaging to obtain the macroscale mass balance equations. We focus on the case of local mass equilibrium conditions where the averaged concentrations in the fluid and biological phases can be assumed to be proportional and for which a one-equation macroscopic model may be developed. We predict the effective dispersion tensor by a closure scheme that is solved for the cases of both simple and complex unit cells. The domain of validity of the approach is clearly identified, both theoretically and numerically, and unitless groupings indicating the domain of validity are reported