Webbased molecular modeling using JAVA/SWARM, J2EE, and RDBMS Technologies

摘要: This paper describes the application of Java/Swarm, J2EE and RDBMS technologies to the area of web-based scientific simulation. One such scientific simulation is on the behavior of natural organic matter (NOM). NOM is a heterogeneous mixture of organic molecules found in terrestrial and aquatic environments-from forest soils and streams to coastal rivers and marshes to the open sea. NOM plays a vital role in ecological and biogeochemical processes. In this paper, we present an agent-based stochastic simulation of NOM transformations, including biological and non-biological reactions, as well as adsorption and physical transport. It employs recent advances in web-based development environments such as Java 2 Enterprise Edition (J2EE), and scalable web-based relational database management systems (RDBMS), to improve the reliability and scalability of the stochastic simulations and to facilitate analysis and data mining of the resulting large datasets. The NOM simulation system may be useful in many areas including chemistry, geology, microbial ecology and environmental science.