## Materials and Methods
### LandscapeDNDC Model Framework
In the case of the PSIM runs with structured canopy, only parameters for canopy trees were adjusted, using literature parameters of ash trees for the understorey vegetation. The simulation is driven by climate input and a management file that includes the timing and intensity of events. The model is run with daily weather data that are internally converted into hourly values to drive the model processes (except tree dimensional changes that were calculated once a year). Weather input for 1995-1998, comprising mean, maximum and minimum air temperature, precipitation, global radiation and wind speed, has been provided by the UK Meteorological Office affiliated climatology station, situated in an open area 1.8 km from the Straits Inclosure site. Since 1999, weather data were directly measured at the Straits EC Tower Site itself and provided model input as listed above, with additional vapour pressure deficit and air pressure data for 1999-2011. Overall, simulations were run from January 1995 to December 2014, with results of the first 4 years discarded from further analysis to avoid effects of potential pool transitions to equilibrium conditions. Regarding management impacts, thinning is considered as a defined number and volume of trees removed at a particular day. At the Straits Inclosure site, a thinning took \begin{table}
\begin{tabular}{c c c c c} \hline \hline
**Parameter** & **Description** & **Units** & **PnET** & **PSIM (Understorey Value)** \\ \hline \multicolumn{5}{c}{**CO\({}_{2}\) exchange parameters**} \\ \hline BASEPOLRESPFRAC & Dark respiration as fraction of photosynthesis & 0-1 & 0.15 & na \\ AMAXB & Maximal net photosynthetic rate & nmol CO\({}_{2}\) g\({}^{-1}\) s\({}^{-1}\)/\(\gamma\)\(\omega\)N & 55 & na \\ RESPQ10 2  & - & 2 & na \\ VCCAX25 & Maximum RubP saturated rate of carboxylation at & \(\mu\)mol m\({}^{-2}\) s\({}^{-1}\) & na & 90 (85) \\  & 25 \({}^{\circ}\)C for leaves in full sun & & & \\ KM20 & Respiration maintenance coefficient at & 0–1 & na & 0.3 (0.1) \\  & reference temperature & & & \\ \hline \multicolumn{5}{c}{**Phenology-related parameters**} \\ \hline GDPOISTART3  & Daily temperature sum for start of foliage budburst & \({}^{\circ}\)days & 500 & 500 (0) \\ GDPOIENDFOOTNOTE 3  & Foliage biomass under optimal, closed & kg DW m\({}^{-2}\) & 0.47 & 0.47 (0.36) \\  & canopy conditions & & & \\  & & & & \\  & & & & \\  & & & & \\  & & & & \\  & & & & \\  & & & & \\ \end{tabular}
\end{table} 
Table 3: LandscapeDNDC vegetation modules’ species parameters adjusted to simulate GHG fluxes for pedunculate oak at the Straits Inclosure. place in September 2007 in the eastern half, removing about 30% of the commercially valuable, main stem timber volume, with foliage and branches left on the ground [45]. Since the thinning was not homogeneously distributed across the site, the effects of 0%, 15% and 30% canopy tree removal were simulated, both to be compared with EC measurements during particular wind directions. The simulation considers that only stem wood was removed and foliar as well as fine root biomass was added to the respective litter pools. In the PSIM simulations, thinning in the understorey was also considered, representing a removal of 0%, 15% and 60%. In contrast to the upper canopy trees, all understorey above ground biomass was left at the site and transferred to litter compartments. No such distinction was made when using PnET. Model output is provided as daily and annual values. GPP is simulated directly as carbon uptake by photosynthesis, while terrestrial ecosystem respiration (TER) is calculated by summing the model output of soil heterotrophic respiration and vegetation autotrophic respiration, composed of carbon releases due to growth and maintenance. Net ecosystem production (NEP) is then calculated as the difference between GPP and TER, which is positive if there is a net uptake of CO\({}_{2}\). Eddy covariance methods conventionally define net ecosystem exchange (NEE) as negative when there is a net uptake of CO\({}_{2}\).