## 2 Materials and Methods  
### Ecosystem Modeling  
A wide variety of models have been developed to evaluate questions related to nitrogen dynamics, with the variation primarily manifested as different levels of complexity, different scales of application, and different questions of interest. These range from 3-dimensional physically-based research models, which are applicable across a broad range of environments and time scales (ecosys; [14]) to lumped data-based techniques (UNERF; [15]), which are reliant upon long term input output measurements, and maintain no physical basis. In this paper we are primarily interested in forested watershed nitrogen dynamics, which represents only a small subset of this broad range of models. For these ecosystems, modeling strategies generally incorporate associated carbon and water cycling, and while there is considerable overlap, the models tend to focus on one of three basic lines of inquiry. The first of these relates to forest productivity and succession. Productivity models are developed primarily to predict the successional evolution of above ground biomass (e.g., 3 PG [16]) or focus on carbon dynamics and primary productivity (e.g., the PnET models [17]). Models in this group tend to include a more robust depiction of primary production, canopy processes, and carbon allocation, with somewhat less detail in terms of soil organic matter processing. The second general class of ecosystem models focuses more heavily on  
Figure 1: A flow chart outlining key model stocks and fluxes. Some minor flux terms have been left out of the figure to improve clarity. Note also that the litter input into aquatic biomass is derived directly from the stocks of foliage and branches/coarse wood.  
soil nutrient cycling and soil organic matter (SOM) dynamics. This group includes many of agricultural models, some of which have been adapted to represent forested landscapes (CENTURY [18]). A third approach focuses not on vegetation or SOM properties, but rather on hydrology and nitrogen export in an effort to provide a predictive tool to quantify nitrogen leaching potential (MERLIN [10]).  
Regional to global scale biogeochemical models, a somewhat different class of simulation tools make use of many of the concepts outlined in the models above, coupling water, carbon, and nitrogen cycles to represent complete regional scale ecosystems. These models display less disciplinary focus, and are used primarily to evaluate the function of whole ecosystems under changing climate or deposition patterns. Representative models in this group include GEM [19] and BIOM-BGC [20] and INCA [21].  
Most of these ecosystem scale models maintain a spatially lumped approach, though a number of spatially distributed simulation tools--those that include lateral interaction terms--have been developed (e.g., RHYSSYS [22]). With the exception of MEL [23] none of these models treat the production or mobility of dissolved organic nitrogen, an oversight representing a potentially significant structural error in terms of potential maximum amounts of sequestered carbon [23]. Additionally, while a variety of aquatic simulation models have been developed [2], these concepts have not been explicitly included in any of the ecosystem models.  
The modeling we developed here relies fundamentally upon a variety of ideas and algorithms proposed within the range of existing ecosystem models. Our intention isn't to replace any of these models, but rather to select elements from them, and to put those elements together to represent a particular location with a particular set of processes.