Plantecophys : an R package for analysing and modelling leaf gas exchange data

Here I present the R package 'plantecophys', a toolkit to analyse and model leaf gas exchange data. Measurements of leaf photosynthesis and transpiration are routinely collected with portable gas exchange instruments, and analysed with a few key models. These models include the Farquhar-von Caemmerer-Berry (FvCB) model of leaf photosynthesis, the Ball-Berry models of stomatal conductance, and the coupled leaf gas exchange model which combines the supply and demand functions for CO2 in the leaf. The 'plantecophys' R package includes functions for fitting these models to measurements, as well as simulating from the fitted models to aid in interpreting experimental data. Here I describe the functionality and implementation of the new package, and give some examples of its use. I briefly describe functions for fitting the FvCB model of photosynthesis to measurements of photosynthesis-CO2 response curves ('A-Ci curves'), fitting Ball-Berry type models, modelling C3 photosynthesis with the coupled photosynthesis-stomatal conductance model, modelling C4 photosynthesis, numerical solution of optimal stomatal behaviour, and energy balance calculations using the Penman-Monteith equation. This open-source package makes technically challenging calculations easily accessible for many users and is freely available on CRAN

Relations between M\"obius and coboundary polynomial

It is known that, in general, the coboundary polynomial and the M\"obius polynomial of a matroid do not determine each other. Less is known about more specific cases. In this paper, we will try to answer if it is possible that the M\"obius polynomial of a matroid, together with the M\"obius polynomial of the dual matroid, define the coboundary polynomial of the matroid. In some cases, the answer is affirmative, and we will give two constructions to determine the coboundary polynomial in these cases.Comment: 12 page

Upside-down fluxes Down Under: CO2 net sink in winter and net source in summer in a temperate evergreen broadleaf forest

Predicting the seasonal dynamics of ecosystem carbon fluxes is challenging in broadleaved evergreen forests because of their moderate climates and subtle changes in canopy phenology. We assessed the climatic and biotic drivers of the seasonality of net ecosystem–atmosphere CO2 exchange (NEE) of a eucalyptus-dominated forest near Sydney, Australia, using the eddy covariance method. The climate is characterised by a mean annual precipitation of 800mm and a mean annual temperature of 18°C, hot summers and mild winters, with highly variable precipitation. In the 4-year study, the ecosystem was a sink each year (−225gCm−2yr−1 on average, with a standard deviation of 108gCm−2yr−1); inter-annual variations were not related to meteorological conditions. Daily net C uptake was always detected during the cooler, drier winter months (June through August), while net C loss occurred during the warmer, wetter summer months (December through February). Gross primary productivity (GPP) seasonality was low, despite longer days with higher light intensity in summer, because vapour pressure deficit (D) and air temperature (Ta) restricted surface conductance during summer while winter temperatures were still high enough to support photosynthesis. Maximum GPP during ideal environmental conditions was significantly correlated with remotely sensed enhanced vegetation index (EVI; r2 = 0.46) and with canopy leaf area index (LAI; r2= 0.29), which increased rapidly after mid-summer rainfall events. Ecosystem respiration (ER) was highest during summer in wet soils and lowest during winter months. ER had larger seasonal amplitude compared to GPP, and therefore drove the seasonal variation of NEE. Because summer carbon uptake may become increasingly limited by atmospheric demand and high temperature, and because ecosystem respiration could be enhanced by rising temperatures, our results suggest the potential for large-scale seasonal shifts in NEE in sclerophyll vegetation under climate change.The Australian Education Investment Fund, Australian Terrestrial Ecosystem Research Network, Australian Research Council and Hawkesbury Institute for the Environment at Western Sydney University supported this work. We thank Jason Beringer, Helen Cleugh, Ray Leuning and Eva van Gorsel for advice and support. Senani Karunaratne provided soil classification details

Applying the concept of ecohydrological equilibrium to predict steady state leaf area index

Leaf area index (LAI) is a key variable in modeling terrestrial vegetation because it has a major impact on carbon and water fluxes. However, several recent intercomparisons have shown that modeled LAI differs significantly among models and between models and satellite‐derived estimates. Empirical studies show that LAI is strongly related to precipitation. This observation is predicted by the ecohydrological equilibrium theory, which provides an alternative means to predict steady state LAI. We implemented this theory in a simple optimization model. We hypothesized that, when water availability is limited, plants should adjust steady state LAI and stomatal behavior to maximize net canopy carbon export, under the constraint that canopy transpiration is a fixed fraction of total precipitation. We evaluated the predicted LAI (Lopt) for Australia against ground‐based observations of LAI at 135 sites and continental‐scale satellite‐derived estimates. For the site‐level data, the root‐mean‐square error of predicted Lopt was 1.07 m2 m−2, similar to the root‐mean‐square error of a comparison of the data against 9‐year mean satellite‐derived LAI (Lsat) at those sites. Continentally, Lopt had an R2 of 0.7 when compared to Lsat. The predicted Lopt increased continental‐wide with rising atmospheric [CO2] over 1982–2010, which agreed with satellite‐derived estimations, while the predicted stomatal behavior responded differently in dry and wet regions. Our results indicate that long‐term equilibrium LAI can be successfully predicted from a simple application of ecohydrological theory. We suggest that this theory could be usefully incorporated into terrestrial vegetation models to improve their predictions of LAI

Testing Hardy nonlocality proof with genuine energy-time entanglement

We show two experimental realizations of Hardy ladder test of quantum nonlocality using energy-time correlated photons, following the scheme proposed by A. Cabello \emph{et al.} [Phys. Rev. Lett. \textbf{102}, 040401 (2009)]. Unlike, previous energy-time Bell experiments, these tests require precise tailored nonmaximally entangled states. One of them is equivalent to the two-setting two-outcome Bell test requiring a minimum detection efficiency. The reported experiments are still affected by the locality and detection loopholes, but are free of the post-selection loophole of previous energy-time and time-bin Bell tests.Comment: 5 pages, revtex4, 6 figure