Web-Based Molecular Simulation using Agent-Based Modeling Techniques


Note: This poster reports on an ongoing study that began at SwarmFest 2002 (Seattle, WA) when one of the investigators presented a research problem and requested opinions on the feasibility of using Swarm on the study. Those opinions, along with practical advice, contributed to the following successful results.

Natural organic matter (NOM), a heterogeneous mixture of molecules, plays a crucial role in the evolution of soils, the transport of pollutants, and the change of global weather. The evolution of NOM over time is an important research area in biology, geochemistry, ecology, soil science, and water resources. Due to its complexity and structural heterogeneity, new simulation approaches are needed to help to better understand the structure and the evolution of NOM. We present a new stochastic model, implemented using Java/Swarm, which explicitly treats NOM as a large number of discrete heterogeneous molecules. The NOM, micro-organisms, and their environment are taken together as a complex system, and simulated using an agent-based modeling approach. The global properties of NOM evolution over time can be studied by simulating the physical and chemical reactions between individual agents with temporal and spatial properties. Unlike the previous stand-alone simulation models, the NOM simulation model serves as an example of E-science, in which we do science on the Web by combining recent information technologies (Java 2 Enterprise Edition, J2EE) with an agent-based computational approach. An intelligent Web-based interface is developed to allow scientists to access the remote simulation model from a standard Web browser. The Web-based interface enables scientists to remotely provide parameters for their simulations, start and stop the simulations, and view the results. The initial users of the NOM simulation model includes a geographically separated group of NSF sponsored scientists from different research areas. A NOM collaboratory is built to promote collaboration among these scientists and allow them to share their data and information across distributed sites. A XML-based Markup Language, NOML, is provided to build the XML-based Web components and facilitate Web services development in the future.

Greg Madey
Computer Science & Engineering
University of Notre Dame
address@hidden