[SwarmFest2004] SwarmFest2004 - Poster Abstact 2

[Greg Madey]

All ... sorry for being late again. I hope you can still accept this?  
This is the last one. Greg

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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

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