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

Reviewing agent-based modelling of socio-ecosystems: a methodology for the analysis of climate change adaptation and sustainability

The integrated - environmental, economic and social - analysis of climate change calls for a paradigm shift as it is fundamentally a problem of complex, bottom-up and multi-agent human behaviour. There is a growing awareness that global environmental change dynamics and the related socio-economic implications involve a degree of complexity that requires an innovative modelling of combined social and ecological systems. Climate change policy can no longer be addressed separately from a broader context of adaptation and sustainability strategies. A vast body of literature on agent-based modelling (ABM) shows its potential to couple social and environmental models, to incorporate the influence of micro-level decision making in the system dynamics and to study the emergence of collective responses to policies. However, there are few publications which concretely apply this methodology to the study of climate change related issues. The analysis of the state of the art reported in this paper supports the idea that today ABM is an appropriate methodology for the bottom-up exploration of climate policies, especially because it can take into account adaptive behaviour and heterogeneity of the system's components.Review, Agent-Based Modelling, Socio-Ecosystems, Climate Change, Adaptation, Complexity.

How Should Life Support Be Modeled and Simulated?

Why do most space life support research groups build and investigate large models for systems simulation? The need for them seems accepted, but are we asking the right questions and solving the real problems? The modeling results leave many questions unanswered. How then should space life support be modeled and simulated? Life support system research and development uses modeling and simulation to study dynamic behavior as part of systems engineering and analysis. It is used to size material flows and buffers and plan contingent operations. A DoD sponsored study used the systems engineering approach to define a set of best practices for modeling and simulation. These best practices describe a systems engineering process of developing and validating requirements, defining and analyzing the model concept, and designing and testing the model. Other general principles for modeling and simulation are presented. Some specific additional advice includes performing a static analysis before developing a dynamic simulation, applying the mass and energy conservation laws, modeling on the appropriate system level, using simplified subsystem representations, designing the model to solve a specific problem, and testing the model on several different problems. Modeling and simulation is necessary in life support design but many problems are outside its scope

Can geocomputation save urban simulation? Throw some agents into the mixture, simmer and wait ...

There are indications that the current generation of simulation models in practical, operational uses has reached the limits of its usefulness under existing specifications. The relative stasis in operational urban modeling contrasts with simulation efforts in other disciplines, where techniques, theories, and ideas drawn from computation and complexity studies are revitalizing the ways in which we conceptualize, understand, and model real-world phenomena. Many of these concepts and methodologies are applicable to operational urban systems simulation. Indeed, in many cases, ideas from computation and complexity studies—often clustered under the collective term of geocomputation, as they apply to geography—are ideally suited to the simulation of urban dynamics. However, there exist several obstructions to their successful use in operational urban geographic simulation, particularly as regards the capacity of these methodologies to handle top-down dynamics in urban systems. This paper presents a framework for developing a hybrid model for urban geographic simulation and discusses some of the imposing barriers against innovation in this field. The framework infuses approaches derived from geocomputation and complexity with standard techniques that have been tried and tested in operational land-use and transport simulation. Macro-scale dynamics that operate from the topdown are handled by traditional land-use and transport models, while micro-scale dynamics that work from the bottom-up are delegated to agent-based models and cellular automata. The two methodologies are fused in a modular fashion using a system of feedback mechanisms. As a proof-of-concept exercise, a micro-model of residential location has been developed with a view to hybridization. The model mixes cellular automata and multi-agent approaches and is formulated so as to interface with meso-models at a higher scale

simecol: An Object-Oriented Framework for Ecological Modeling in R

The simecol package provides an open structure to implement, simulate and share ecological models. A generalized object-oriented architecture improves readability and potential code re-use of models and makes simecol-models freely extendable and simple to use. The simecol package was implemented in the S4 class system of the programming language R. Reference applications, e.g. predator-prey models or grid models are provided which can be used as a starting point for own developments. Compact example applications and the complete code of an individual-based model of the water flea Daphnia document the efficient usage of simecol for various purposes in ecological modeling, e.g. scenario analysis, stochastic simulations and individual based population dynamics. Ecologists are encouraged to exploit the abilities of simecol to structure their work and to use R and object-oriented programming as a suitable medium for the distribution and share of ecological modeling code.

An open and extensible framework for spatially explicit land use change modelling in R: the lulccR package (0.1.0)

Land use change has important consequences for biodiversity and the sustainability of ecosystem services, as well as for global environmental change. Spatially explicit land use change models improve our understanding of the processes driving change and make predictions about the quantity and location of future and past change. Here we present the lulccR package, an object-oriented framework for land use change modelling written in the R programming language. The contribution of the work is to resolve the following limitations associated with the current land use change modelling paradigm: (1) the source code for model implementations is frequently unavailable, severely compromising the reproducibility of scientific results and making it impossible for members of the community to improve or adapt models for their own purposes; (2) ensemble experiments to capture model structural uncertainty are difficult because of fundamental differences between implementations of different models; (3) different aspects of the modelling procedure must be performed in different environments because existing applications usually only perform the spatial allocation of change. The package includes a stochastic ordered allocation procedure as well as an implementation of the widely used CLUE-S algorithm. We demonstrate its functionality by simulating land use change at the Plum Island Ecosystems site, using a dataset included with the package. It is envisaged that lulccR will enable future model development and comparison within an open environment

Theories about architecture and performance of multi-agent systems

Multi-agent systems are promising as models of organization because they are based on the idea that most work in human organizations is done based on intelligence, communication, cooperation, and massive parallel processing. They offer an alternative for system theories of organization, which are rather abstract of nature and do not pay attention to the agent level. In contrast, classical organization theories offer a rather rich source of inspiration for developing multi-agent models because of their focus on the agent level. This paper studies the plausibility of theoretical choices in the construction of multi-agent systems. Multi-agent systems have to be plausible from a philosophical, psychological, and organizational point of view. For each of these points of view, alternative theories exist. Philosophically, the organization can be seen from the viewpoints of realism and constructivism. Psychologically, several agent types can be distinguished. A main problem in the construction of psychologically plausible computer agents is the integration of response function systems with representational systems. Organizationally, we study aspects of the architecture of multi-agent systems, namely topology, system function decomposition, coordination and synchronization of agent processes, and distribution of knowledge and language characteristics among agents. For each of these aspects, several theoretical perspectives exist.