## 2 Materials and Methods
### The HJA-N Model
#### 2.3.3 Vegetation Model  
Carbon and nitrogen in pools representing wood, foliage, and fine roots are included in the model. The woody pool includes coarse roots, logs, as well as branches (Table 9). The three pools were utilized primarily because they are consistent with a variety of measurements that have been made at HJA and because they are functionally useful in that CN ratios and decomposition rates from these three pools are distinct. Biomass production follows closely from the 3-PG model [16]. Gross primary production (GPP) is estimated based upon measured net shortwave radiation and using a simple empirical relationship between shortwave radiation and the photosynthetically active fraction (PAR). [PERSON]'s law is utilized to approximate light attenuation through the single layer canopy and the fraction of incident PAR absorbed by the vegetation. The leaf area index (LAI) is calculated based upon the simulated foliar biomass, where the specific leaf area is assumed to be a species dependent constant. A collection of five functional modifiers are utilized to reflect role of environmental conditions in limiting the quantity of absorbed radiation utilized by the vegetation. These modifiers relate to soil moisture, vapor pressure deficit, stand age, air temperature, and in an extension of the original 3-PG concept [16], we have also included the availability of plant-available nitrogen in the root zone. The resulting estimate of utilized radiation governs, in combination with an estimate of canopy quantum efficiency, the estimated GPP. Net primary production (NPP) is then estimated as a constant fraction of GPP. Live allocation of NPP (as carbon) to the three major biomass stocks follows from [16]. Nitrogen storages follow from the production of carbon, and are based on targeted CN ratios for each of the pools. NPP is initially allocated to fine roots, as a function of absorbed and utilized radiation. More limiting growth conditions (captured as the five modifiers defined above and resulting in utilized radiation) result in a larger allocation to roots, following directly from [19]. After fine root NPP is calculated, the remaining fraction NPP is allocated to woody material and foliage using set fractions developed to maintain targeted CN ratios of wood and foliage. Uptake of N is a rate term which transfers mass from the dissolved inorganic nitrogen (DIN) pool into the living biomass N pools. This rate term is similar to that employed within MERLIN [10]. Michaelis-Menten kinetics are used to develop a non-linear rate which depends upon DIN availability and also plant nutritional requirements (see Table 4), as inferred from NPP and the targeted CN ratio of the three vegetation pools. The dependence of uptake on production is incorporated by allowing \(K_{\text{Nup}}\) to vary linearly with NPP. The rate of change, or the \(\
icefrac{{1}}{{2}}\) saturation constant likely varies in time, dependent upon the plant CN ratio [8], however the additional complexity is not incorporated into the current model. \(N_{\text{up}}\) is allocated to each of the three live biomass storages based upon deviations of the current CN ratios from target live CN ratios (defined as CN/CN\({}_{\text{t}}\)) for the fine root components. As the CN ratio for the fine roots deviates further from the targeted value, a larger percentage of \(N_{\text{up}}\) is allocated to the fine roots. The portion of \(N_{\text{up}}\) which is not allocated to the fine roots is portioned between the wood and foliar components based upon a constant allocation fraction. Stoichiometric N requirements of living biomass are also satisfied through N fixation, which occurs primarily in the canopy, given the presence of lichen. The rate of symbiotic fixation is calculated using a maximum fixation rate modified using the air temperature modifier [26]. Nitrogen fixed within the canopy is distributed based upon the nitrogen allocation fractions. Nitrogen is also introduced into the system through asymbiotic fixation, calculated analogously to symbiotic fixation.