A comparative analysis of parallel processing and super-individual methods for improving the computational performance of a large individual-based model

Individual-based modelling approaches are being used to simulate larger complex spatial systems in ecology and in other fields of research. Several novel model development issues now face researchers: in particular how to simulate large numbers of individuals with high levels of complexity, given finite computing resources. A case study of a spatially-explicit simulation of aphid population dynamics was used to assess two strategies for coping with a large number of individuals: the use of ‘super-individuals’ and parallel computing. Parallelisation of the model maintained the model structure and thus the simulation results were comparable to the original model. However, the super-individual implementation of the model caused significant changes to the model dynamics, both spatially and temporally. When super-individuals represented more than around 10 individuals it became evident that aggregate statistics generated from a super-individual model can hide more detailed deviations from an individual-level model. Improvements in memory use and model speed were perceived with both approaches. For the parallel approach, significant speed-up was only achieved when more than five processors were used and memory availability was only increased once five or more processors were used. The super-individual approach has potential to improve model speed and memory use dramatically, however this paper cautions the use of this approach for a density-dependent spatially-explicit model, unless individual variability is better taken into account

A State-of-the-art Integrated Transportation Simulation Platform

Nowadays, universities and companies have a huge need for simulation and modelling methodologies. In the particular case of traffic and transportation, making physical modifications to the real traffic networks could be highly expensive, dependent on political decisions and could be highly disruptive to the environment. However, while studying a specific domain or problem, analysing a problem through simulation may not be trivial and may need several simulation tools, hence raising interoperability issues. To overcome these problems, we propose an agent-directed transportation simulation platform, through the cloud, by means of services. We intend to use the IEEE standard HLA (High Level Architecture) for simulators interoperability and agents for controlling and coordination. Our motivations are to allow multiresolution analysis of complex domains, to allow experts to collaborate on the analysis of a common problem and to allow co-simulation and synergy of different application domains. This paper will start by presenting some preliminary background concepts to help better understand the scope of this work. After that, the results of a literature review is shown. Finally, the general architecture of a transportation simulation platform is proposed

Travelling wave solutions in a negative nonlinear diffusion-reaction model

We use a geometric approach to prove the existence of smooth travelling wave solutions of a nonlinear diffusion-reaction equation with logistic kinetics and a convex nonlinear diffusivity function which changes sign twice in our domain of interest. We determine the minimum wave speed, c*, and investigate its relation to the spectral stability of the travelling wave solutions.Comment: 23 pages, 10 figure

Species abundance patterns in an ecosystem simulation studied through Fisher's logseries

We have developed an individual-based evolving predator-prey ecosystem simulation that integrates, for the first time, a complex individual behaviour model, an evolutionary mechanism and a speciation process, at an acceptable computational cost. In this article, we analyse the species abundance patterns observed in the communities generated by our simulation, based on Fisher's logseries. We propose a rigorous methodology for testing abundance data against the logseries. We show that our simulation produces coherent results, in terms of relative species abundance, when compared to classical ecological patterns. Some preliminary results are also provided about how our simulation is supporting ecological field results

Review of trace toxic elements (Pb, Cd, Hg, As, Sb, Bi, Se, Te) and their deportment in gold processing. Part 1: Mineralogy, aqueous chemistry and toxicity

A literature review on the deportment of trace toxic elements (Pb, Cd, Hg, As, Sb, Bi, Se, and Te) in gold processing by cyanidation is presented which compiles the current knowledge in this area and highlights the gaps. This review, together with further research on the gaps in the thermodynamics and kinetics of these systems, aims to support the development of computer models to predict the chemical speciation and deportment of these elements through the various stages of the gold cyanidation process. The first part of this review is a collation of the relevant information on trace element mineralogy, aqueous chemistry and toxicity, together with a comparison of two available software packages (JESS and OLI) for thermodynamic modelling. Chemical speciation modelling can assist in understanding the chemistry of the trace toxic elements in gold cyanidation solutions which remains largely unexplored. Many significant differences exist between the predicted speciation of these trace elements for different types of modelling software due to differences in the thermodynamic data used, the paucity of data that exists under appropriate non-ideal conditions, and the methods used by the software packages to estimate thermodynamic parameters under these conditions. The toxicity and environmental guidelines of the chosen trace element species that exist in aqueous solutions are discussed to better understand the health and environmental risks associated with the presence of these elements in gold ores

Volume of the steady-state space of financial flows in a monetary stock-flow-consistent model

We show that a steady-state stock-flow consistent macro-economic model can be represented as a Constraint Satisfaction Problem (CSP).The set of solutions is a polytope, which volume depends on the constraintsapplied and reveals the potential fragility of the economic circuit,with no need to study the dynamics. Several methods to compute the volume are compared, inspired by operations research methods and theanalysis of metabolic networks, both exact and approximate.We also introduce a random transaction matrix, and study the particularcase of linear flows with respect to money stocks