Building modular FSPM under OpenAlea: concepts and applications

International audienceThe OpenAlea platform (Pradal et al., 2008) was designed to facilitate the integration and inter-operability of heterogeneous models to get comprehensive FSPMs. It relies on Python gluing capabilities, that allow non intrusive integration of programs written in various languages (Fortran, C, C++, R, L-system); and on the dataflow computing paradigm, that promotes decomposition of applications into independent components that can be recombined dynamically into customized workflows. Still, a plugable collection of components is not by itself a solution to the modularity problem in FSPM modeling. First, heterogeneities between components inputs and outputs can lead to exponential needs for specific adaptors and converters to get functional assemblies. Second, several ways exist to decompose models into independent components. This can lead to incompatibilities or difficulties for re-assembly into comprehensive models. Last, users of the platform may find difficult to build applications, without some knowledge on how a simulation has to be reasoned within the data-flow computing paradigm. Here, we propose a modeling strategy to help for building coherent, yet modular FSPM under OpenAlea. We first define the key concepts of this strategy, illustrate how they can be used under Visualea and how it lead to a first set of reusable components resulting from various ecophysiological studies

Toward the inter-comparison of radiation transfer model for plant modelling application

The simulation of radiation transfer (RT) is used in many FSPM models and applications. This preeminence is explained by the central role of light in plant growth and development, light being both the energetic source of photosynthesis and an important mediator for the adaptation of plant development to their environment (photomorphogenesis). Radiation is also a key component of the energy budget of plant organs and a factor driving stomata. Thus RT models are required to simulate organ temperature, transpiration and the simulation of water fluxes within plants. At a larger scale, radiation transfer models allow to quantify the light interception efficiency of complex tree crowns or of a canopy, which are important traits for breeding or crop modelling. They also makes it possible to determine the sharing of light between different individuals and species within natural and artificial plant communities; both in field or controlled conditions. Parallel to this variety of applications, different RT models were developed or adapted for use in the FSPM community. They differ both on the way they apprehend plant geometry (volumic vs surfacic objects) and on the way they approximate the physics of radiation transfers and light-plant interactions. The aim of this paper is to provide a practical help to modelers for choosing, correctly use and compare RT models for a given application. Based on a synthetic view of the rationale of the principal approaches used in RT models, we identified and standardised the different types of inputs of RT models, and proposed a unified interface for running them. Second, we defined several simulation scenarios that cover the main applications cited above, both for crop and tree plants (wheat, maize, apple tree, communities of grassland plants). For each scenario, four different models (Caribu, RATP, Muslim, Fractalysis), that covers a large range of approaches are run and compared on pre-defined target variables. All models and scenarios are available on the OpenAlea platform, and can be connected as components with others models. Models are provided as plugins of a common service that expose radiation models with a uniform interface. New RT models can be added dynamically and compared with others. The comparison includes an estimation of bias and errors, as well as its efficiency in terms of computational time. This work is a first initiative towards a benchmark proposal, open to the whole FSPM community, similar to the RAMI initiative for the inter-comparison of radiation transfer model for remote sensing application. (Texte intégral

Metamorphosis-Induced Changes in the Coupling of Spinal Thoraco-Lumbar Motor Outputs During Swimming in Xenopus laevis

International audienceBeyeler A, Métais C, Combes D, Simmers J, Le Ray D. Metamorphosis induced changes in the coupling of spinal thoraco-lumbar motor outputs during swimming in Xenopus laevis. Anuran metamorphosis includes a complete remodeling of the animal's biomechanical apparatus, requiring a corresponding functional reorganization of underlying central neural circuitry. This involves changes that must occur in the coordination between the motor outputs of different spinal segments to harmonize locomotor and postural functions as the limbs grow and the tail regresses. In premetamorphic Xenopus laevis tadpoles, axial motor output drives rostrocaudally propagating segmental myotomal contractions that generate propulsive body undulations. During metamorphosis, the anterior axial musculature of the tadpole progressively evolves into dorsal muscles in the postmetamorphic froglet in which some of these back muscles lose their implicit locomotor function to serve exclusively in postural control in the adult. To understand how locomotor and postural systems interact during locomotion in juvenile Xenopus, we have investigated the coordination between postural back and hindlimb muscle activity during free forward swimming. Axial/ dorsal muscles, which contract in bilateral alternation during undulatory swimming in premetamorphic tadpoles, change their left-right coordination to become activated in phase with bilaterally synchronous hindlimb extensions in locomoting juveniles. Based on in vitro electrophysiologi-cal experiments as well as specific spinal lesions in vivo, a spinal cord region was delimited in which propriospinal interactions are directly responsible for the coordination between leg and back muscle contractions. Our findings therefore indicate that dynamic postural adjustments during adult Xenopus locomotion are mediated by local intraspinal pathways through which the lumbar generator for hindlimb propulsive kicking provides caudorostral commands to thoracic spinal circuitry controlling the dorsal trunk musculature

Representation and functions of shoot apical meristems in FSPMs

Functional Structural Plant Models (FSPMs) are individual-based models that explicitly account for the interactions between plant architecture and its abiotic and biotic environment. Plant morphogenesis, growth and grain or fruit production are among the most represented processes in FSPMs. These biological processes are largely determined at the Shoot Apical Meristem (SAM) level as it drives the rate of leaf initiation, phyllotaxy, leaf geometry, floral induction and the production of reproductive organs. Nevertheless, not all FSPMs are based on an explicit representation of SAMs, their functioning is then ignored in the case of non-dynamic models or embedded in parametric or statistical functions of plant morphogenesis in dynamic models. For FSPMs that include an explicit representation of SAMs, they are mainly constructed on the L-systems formalism, which is well suited to describe plant development (Boudon et al., 2012). First, one of the main functions of SAMs in these FSPMs is the production of new leaves or growth units, usually at a constant rate expressed in thermal unit. In some cases, the rate of leaf production by SAMs is coordinated with the rate of leaf emergence, leading to the concept of self-regulated architecture. However, the effect of substrate or water availability on the functioning of the SAM in terms of the size or properties of the emitted primordia is not accounting for. Secondly, the representation of apices in models is also used to simulate axillary bud break and the production of tillers, branches or new growth units. In these cases, the transition from a latent to an active SAM is controlled by light intensity and its spectrum (Verdenal et al., 2008; Faverjon et al., 2019), or temperature or hormones (Prusinkiewicz et al., 2009) or is based on stochastic approaches. Finally, some FSPMs also account for the production of reproductive organs like grains and fruits by SAMs (Boudon et al., 2020; Rouet et al., 2022). Nevertheless, this aspect of SAM functioning remains poorly described in FSPMs despite its importance in plant production, yield and ecology. We believe that a better integration of SAMs functioning and control in FSPMs is a promising way to assess functional hypotheses and predict plant plasticity to the environment

Quantum dynamics of simultaneously measured non-commuting observables.

In quantum mechanics, measurements cause wavefunction collapse that yields precise outcomes, whereas for non-commuting observables such as position and momentum Heisenberg's uncertainty principle limits the intrinsic precision of a state. Although theoretical work has demonstrated that it should be possible to perform simultaneous non-commuting measurements and has revealed the limits on measurement outcomes, only recently has the dynamics of the quantum state been discussed. To realize this unexplored regime, we simultaneously apply two continuous quantum non-demolition probes of non-commuting observables to a superconducting qubit. We implement multiple readout channels by coupling the qubit to multiple modes of a cavity. To control the measurement observables, we implement a 'single quadrature' measurement by driving the qubit and applying cavity sidebands with a relative phase that sets the observable. Here, we use this approach to show that the uncertainty principle governs the dynamics of the wavefunction by enforcing a lower bound on the measurement-induced disturbance. Consequently, as we transition from measuring identical to measuring non-commuting observables, the dynamics make a smooth transition from standard wavefunction collapse to localized persistent diffusion and then to isotropic persistent diffusion. Although the evolution of the state differs markedly from that of a conventional measurement, information about both non-commuting observables is extracted by keeping track of the time ordering of the measurement record, enabling quantum state tomography without alternating measurements. Our work creates novel capabilities for quantum control, including rapid state purification, adaptive measurement, measurement-based state steering and continuous quantum error correction. As physical systems often interact continuously with their environment via non-commuting degrees of freedom, our work offers a way to study how notions of contemporary quantum foundations arise in such settings

Simulating light quantity and quality over plant organs using a ray-tracing method to investigate plant responses in growth chambers

Ray-tracing models enable the assessment of light quantity and quality intercepted by plant organs, supporting biological studies in growth chambers with varying light conditions. However, their validation within canopies and clear usage methods remain limited. This work establishes a reliable method for using these models. The method includes i) accounting for the intensity and spectrum of light sources in the calibration procedure; ii) a generic calibration strategy using a few well-placed light measurement points based on chamber geometry. It evaluates the method to simulate light phylloclimate at the organ scale across biologically relevant wavebands of contrasted widths and properties. Using the SEC2 light simulation framework, three virtual experiments were conducted in a growth chamber, with and without rose plants. Inputs included chamber geometry, material optical properties, lamp emissions, and digitised plant mock-ups. Simulations were compared with spectral measurements at various chamber positions and sensor orientations, both without plants and inside a canopy. Results showed high accuracy in replicating spatial light variability, with RMSE ranging 0.011 to 0.021 and 0.014–0.038 μmol m-2s-1nm-1 across different wavebands and sensor orientations, for vertical and horizontal transects, respectively. Applying this approach to a case study demonstrated its effectiveness in formulating new biological hypotheses regarding the role of local light in regulating bud outgrowth. This was achieved by highlighting differences in phylloclimate induced by variations in plant architecture. This work thus provides a comprehensive framework for facilitating the application of ray-tracing models in growth chamber studies