FSPM2013 Proceedings

Foreword

Anna Lintunen — Mon, 03 Jun 2013 11:15:39 +0300

KEYNOTE: Functional-structural modelling with L-systems: Where from and where to

Jim Hanan — Mon, 03 Jun 2013 10:27:40 +0300

The L-systems formalism with turtle interpretation captures plant structural topology and geometry, signalling within the branching structure, and development over time, forming a basis for plant modelling languages. With the addition of environmental interfaces, they have been successfully used to model a variety of plants. Areas for future development include integration of different aspects of plant function, multi-scale modelling and development as a platform for further simulation.

Biomechanics of Bark Patterning in Grasstree

Holly Jennifer Dale, Adam Runions, David Hobill, Przemyslaw Prusinkiewicz — Mon, 03 Jun 2013 10:29:41 +0300

Bark patterns are a visually important characteristic of trees, attributed to fractures caused by secondary growth of the trunk and branches. A detailed understanding of bark patterns has been impeded by insufficient information regarding biomechanical properties of bark and the corresponding difficulties in faithfully modeling bark fractures using continuum mechanics. Here we focus on grasstrees, which have an unusual bark-like structure composed of distinct leaf bases connected by sticky resin. Due to its discrete character, this structure is exceptionally well suited for computational studies. We created a dynamic grasstree model, which captures both the phyllotactic patterning of the leaf bases during primary growth and the emergence of fractures due to secondary growth. The model reproduces key features of grasstree bark patterns, including inhomogeneities due to compression of leaf bases at the sites of inflorescences.

Floral phyllotaxis of magnolia in computer simulations - towards understanding phyllotactic fingerprint

Beata Zagórska-Marek, Marta Fijak — Mon, 03 Jun 2013 10:30:43 +0300

Magnolia’s floral shoot, with its uniquely rich and diverse phyllotaxis, has been modeled with application of a special program based on geometric model of phyllotaxis. First survey of phyllotactic diversity obtained in the library of 1200 computer simulations proved that, besides the most common main Fibonacci, also other patterns, frequently encountered in nature, such as Lucas and bijugy, are readily formed. This is a part of extensive studies aimed to elucidate the mechanism of phyllotactic fingerprint – the species or genet specific pattern of phyllotactic diversity, first in magnolia flowers and then in other plant structures and taxa.

Modelling the spatial arrangement of vascular bundles in plants

Fabrizio Carteni, Francesco Giannino, Gianni Boris Pezzatti, Stefano Mazzoleni — Mon, 03 Jun 2013 10:31:39 +0300

The spatial arrangement of vascular bundles varies between plant species and organs. A novel reaction-diffusion 2D model is presented defining a set of logical and functional rules able to simulate the differentiation of procambium, phloem and xylem. the model shows that a common mechanism, lying behind the formation of vascular tissues, is able to qualitatively reproduce most stelar structures observed.

Estimating the genetic value of F1 apple progenies for irregular bearing during first years of production

Mon, 03 Jun 2013 10:32:50 +0300

Flowering regularity in apple trees during the beginning of their mature phase was assessed using new descriptors based on annual yields. To allow genotype evaluation at reasonable sampling costs, they were approximated using subsamples of annual shoot sequences at axis scale. The approximation provided a good discrimination between regular and alternate bearing genotypes. QTLs were detected for some descriptors.

Biomechanical modelation of Ravenala madagascariensis petiole

Andres Valencia, Diego Celentano, Paulina Fernandez — Mon, 03 Jun 2013 10:34:29 +0300

The use of shape transformers methodology, local buckling Brazier model and finite elements analysisis to model the Ravenala madagascariensis petiole allows to discover how the relation between shape and mater gives to the plant a structural support to bear high bending and torsion loads without fail. The combination of an elliptical stiff perimeter (epidermis) reinforced with a highly ordered cellular core (aerenchyma) gives to Ravenala petiole two very efficient and secure stability mechanisms.

Modeling and analyzing the topology development of young michelia chapensis

Dong Li, Mengzhen Kang, Philippe de Reffye — Mon, 03 Jun 2013 10:38:11 +0300

Michelia chapensis is one of the most important landscape trees and it is important to study the plant topology structure.

We measured the 2 years old michelia tree through one year, study the tree topology structure, well fit and simulate the tree with the new GreenLab version.

Automated Parameter Estimation for a Plant Architecture Model

Florian Schöler, Jenny Balfer, Volker Steinhage — Mon, 03 Jun 2013 10:39:07 +0300

We present an automated procedure for the creation of architectural plant models. It uses an algorithm for the computation of skeletons from sensor data. The skeletons are annotated with semantic labels for the extraction of architectural parameters. The values of several samples are averaged and serve as the basis for the model, which is implemented as a Relational Growth Grammar.

Modeling the blade shape of landscape trees

Fuping Lin, Dong Li, Xiujuan Wang, Haoyu Wang, Xueqiang Shi — Mon, 03 Jun 2013 10:39:49 +0300

In this study,About 5 blades were sampled and measured with a 3d digitizer (FastSCAN Scorpion, Polhemus, USA). The 3d blade models were then built. We made a coding to read the scanned file, obtained the coordinate data of blade margin through the mouse interaction programme, and then transformed the coordinates into 2d data, normalized the data and got the blade shape.

Biomass-based rapeseed (Brassica napus L.) leaf geometric parameter model

Mon, 03 Jun 2013 10:41:20 +0300

A biomass-based model of leaf geometric parameters of rapeseed was developed, and the effects of cultivars and environmental conditions on rapeseed leaf morphogenesis were considered through the connection to rapeseed growth model via biomass.

Optimize Tree Shape: Targeting for Best Light Interception

Jing Hua, MengZhen Kang — Mon, 03 Jun 2013 10:42:19 +0300

It is assumed that plants have a certain kind of fitness so they can optimize their behaviour to maintain a specific target. Optimization algorithm is used to find tree shape that can maximize the light interception. The shape we got is reasonable and looks like a real tree, which proves partly the fitness of plants.

A novel plant cell division algorithm based on ellipse/ellipsoid fitting

Mon, 03 Jun 2013 10:43:17 +0300

Highlights: A novel plant cell division algorithm is presented for both 2D and 3D representation of cells. The position and orientation of the dividing cell wall were determined by fitting ellipse/ellipsoid to the cell vertices. The new wall is then inserted along the minor diameter of the fitted ellipse/ellipsoid perpendicular to the major diameter of the fitted ellipse/ellipsoid.

Modeling Cucumber leaf orientation as growing in heterogeneous

Qian Tingting, Zhao Chunjiang, Guo Xinyu, Lu Shenglian — Mon, 03 Jun 2013 10:44:35 +0300

The objective of this work is to analyze the changes of leaf azimuth during cucumber growth and describe the relationship between light environment and leaf azimuth character using a simplified model. Five plant density treatments were conducted in autumn 2012. Eight neighboring plants per treatment were selected to measure leaf azimuth, leaf length and leaf width at four times. LAI was considered as indication of light intensity to analyze the relationship between light environment and leaf azimuth character. Linear function was used to describe the relationship between LAI and leaf distribution frequency in different leaf orientation classes. Leaf distribution frequency changed as the influence of heterogeneous light conditions. The leaf distribution frequency in the north direction decreased as LAI increased while opposite situation has been found the south direction.

A combined method for quantifying 3D root architecture of field-grown maize

Jie Wu, Bo Yang, Yan Guo — Mon, 03 Jun 2013 11:56:12 +0300

A new method for reconstructing 3D root architecture of field-grown maize was developed through integrating the spatial deployment of maize axile roots determined by digitizing in situ in the field with geometrical and topological information of scanned lateral roots. Spatial root length density and other root traits of maize can be estimated basing on this integrated method.

Semantic Skeletonization for Structural Plant Analysis

Jenny Balfer, Florian Schöler, Volker Steinhage — Mon, 03 Jun 2013 11:57:27 +0300

Computational plant modeling from 3D sensor data is crucial for the early assessment of plant traits. Semantic modeling enables the incorporation of knowledge about the plant species, leading to an improvement of purely geometrical skeletonization approaches. Structural plant features can thereby robustly be extracted from the sensor data.

PlantScan™: a three-dimensional phenotyping platform for capturing the structural dynamic of plant development and growth

Mon, 03 Jun 2013 11:58:45 +0300

PlantScan is an integrated analysis pipeline, seamlessly integrating hardware and software tools to provide automated, non-invasive analyses of plant structure (topology, surface orientation, number of leaves...), morphology (leaf size, shape, colour, area, volume...) and function. By utilising cutting edge information technology to automatically digitise plants in three dimensions, it enables plant scientists to better understand the complex interactions involved in plant growth, i.e., the plant's genetic make-up, its physical characteristics and the environment in which it grows, thus, providing essential information to populate functional structural plant models.

Improving branch distribution models in trees using X-ray computed tomography

Emmanuel Duchateau, David Auty, Frédéric Mothe, Alexis Achim — Mon, 03 Jun 2013 11:59:51 +0300

The use of external measurements to describe the distribution of branches on tree stems can induce imprecision and bias in estimates of both the number of growth units and the azimuthal distribution of branches. The scanning of logs using X-ray computed tomography yielded knot data that allowed for more accurate identification of the limits of each growth unit. Such information, in conjunction with current models of tree architecture, can be incorporated into functional-structural models describing relationships between tree morphology and biological processes.

tLiDAR methodologies can overcome limitations in estimating forest canopy LAI from conventional hemispherical photograph analyses

Eric Casella, Mathias Disney, James Morison, Helen McKay — Mon, 03 Jun 2013 12:02:43 +0300

The hemispherical photography technique has been widely used to assess the three-dimensional reconstruction quality of virtual plant canopy architectures [1]. High-resolution terrestrial Light Detection And Ranging (tLiDAR) has recently been applied for measuring the 3-D characteristics of forest vegetation [2] and specifically the extraction of canopy directional gap fraction [3]. In contrast with the digital hemispherical photography method, sky conditions appear to have little influence on the quality of the data collected by the tLiDAR technique. This study considers the resolution used during both point cloud data acquisition and the computation of equiangular hemispherical images, which may influence the resolving power of this technique in estimating gaps in a forest environment.

Shape reconstruction of fruit tree from colored 3D point cloud

Shenglian Lu, Xinyu Guo, Chunjiang Zhao, Weiliang Wen, Jianjun Du — Mon, 03 Jun 2013 12:04:48 +0300

A method for automatic and accurate reconstructing the structure of fruit tree from laser scanner measured colored point cloud was presented. The color characteristics of different organ were used as rules to segment point cloud into small point cloud. A skeleton of the tree was then extracted from some small point cloud, and 3D reconstruction was achieved by combining some distribution model of leaf and shoot.

Optimal 3D reconstruction of plants canopy from terrestrial laser scanner data by fusion of the 3D point information and the intensity value

Mathilde Aline Balduzzi, Frédéric Boudon, Christophe Godin — Mon, 03 Jun 2013 12:06:39 +0300

We develop an algorithm to digitize in situ canopy and to tag automatically each of its leaves. This algorithm fuses the distance information and the intensity values of a terrestrial LiDAR scanner.

Bayes trees and forests: combining precise empirical and theoretical tree models

Mon, 03 Jun 2013 12:08:30 +0300

With the new analysis methods for TLS scans, there will be a growing and improving database of 3D descriptions of trees and forest stands. The attributes determining these descriptions can be represented as Bayesian probability distributions, with functional-structural models providing the prior information. These distributions can then be used to create versions of new realistic Bayes forests, where none of the trees are copied from data, but the structure of each is drawn from the data-based distributions. Repeated TLS measurements add a fourth dimension, time, to the mathematical modelling; in this way, we can simulate functional 4D Bayes forests. As in the modelling of the 3D structure, forest models and regularities of growth and mortality are used as prior information; conversely, the accumulating data and modelling results improve the theoretical models.

Quantitative assessement of automatic reconstructions of branching systems

Mon, 03 Jun 2013 12:09:41 +0300

In this work, we propose a method to evaluate and compare different reconstruction methods from laser data using expert reconstruction and a new structural distance.

Rank distributions and biomass partitioning of plants

Alexander S. Komarov, Elena V. Zubkova, Maija Salemaa, Raisa Mäkipää — Mon, 03 Jun 2013 12:32:12 +0300

We study how well biomass partitioning patterns of plant compartments (organs) follow mathematical rank distributions using empirical data from the tree and dwarf shrub species in temperate-boreal zone as a test material. The simplest form of a rank distribution (Zipf’s law) shows a good statistical fit to the data and its semi-empirical dependencies can successfully be applied also in a complex ecosystem models.

Inference of structural plant growth from discrete samples

Christoph Stocker, Franz Uhrmann, Oliver Scholz — Mon, 03 Jun 2013 12:33:52 +0300

We present an approach for the rapid generation of plant growth models from a series of explicit growth stages. Multiple structural plant descriptions, which can be gained from 3D scans, are automatically inferred to an L-system grammar. Morphological leaf features are incorporated into this model by parameterization of the structural description.

A spectral clustering approach of vegetation components for describing plant topology and geometry from terrestrial waveform LiDAR data

Dobrina Boltcheva, Eric Casella, Rémy Cumont, Franck Hétroy — Mon, 03 Jun 2013 12:36:14 +0300

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Modeling and analyzing rice canopies of different cultivars and densities by 3D digitizing method

Dong Li, Zhifu Xu, Shihua Cheng, Liyong Cao — Mon, 03 Jun 2013 12:41:39 +0300

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The use of x-ray computed tomography for creating computational models of corn stalks and other plants: advantages, benefits, and common challenges.

Douglas Cook, Margaret Julias — Mon, 03 Jun 2013 12:49:00 +0300

X-ray computed tomography (CT scanning) is a powerful tool for evaluating plant tissue, and is commonly applied in the field of biomechanics to obtain 3D representations of bone, arteries, and other anatomical data. We have applied this technique to the development of computational models of corn stalks and bamboo culms. While CT scanning has many advantages, the process of creating parsimonious models based on CT data is often challenging since this technique often produces several gigabytes of data for each scan. This paper provides an overview of the advantages, benefits, and common challenges associated with the use of computed tomography in plant modeling in the context of modeling corn stalks.

A Model-based Approach to Extract Leaf Features from 3D Scans

Mon, 03 Jun 2013 12:50:44 +0300

We present a flexible and robust method for the extraction of leaf features from 3D point clouds. An adaptable leaf model is automatically fitted to the measured data in order to obtain a precise but compact parameterization of the leaf shape. As an application example the detection of stress using the fitted leaf parameters is demonstrated.

Root growth and distribution of gooseberry (Physalis peruviana) under field conditions in the Andean soil

Gabriel Roveda, Liz Patricia Moreno Fonseca — Mon, 03 Jun 2013 12:52:35 +0300

A field technology with the computer model called “RACINE” was used to estimate root-length density (RLD) and the root exploration from root count on soil profiles. The results indicated a drastic reduction on root development due to restrictions as low phosphorous and decreasing organic matter. However, Glomus mosse can promote the root system, on RLD and root front.

Defining a reliability coefficient in an automated method of identification of radial files in microscopic images of gymnosperms

Guilhem Brunel, Philippe Borianne, Marc Jaeger, Gérard Subsol, Yves Caraglio — Mon, 03 Jun 2013 12:54:06 +0300

Analysis of wood anatomical sections is of great interest in understanding the growth and development of plants. We propose a novel method to automatically identify and characterize radial files in wood microscopic images of gymnosperms. A key-point is to be able to assign a priori reliability coefficient to the results, in particular in the case of a statistical processing in great-scale analysis. We describe in this paper the building principle of the reliability coefficients to evaluate the radial file identification (process) and the geometrical measurements of the cells and its components.

An automated image-processing pipeline for high-throughput analysis of root architecture in OpenAlea

Mon, 03 Jun 2013 12:56:16 +0300

FSPM analysis of root systems requires structural data obtained on large data set. This paper describes a processing pipeline developed to extract automatically the architecture of root system from images databases.

Terrestrial LiDAR-based tree/stand model that can simulate light interception and photosynthesis of branches, individuals, and a stand

Kiyoshi Umeki, Akira Kato — Mon, 03 Jun 2013 13:16:15 +0300

We developed a tree/stand model that simulates light interception and photosynthesis of first-order branches individuals, and a stand. The architecture of modelled trees was generated using tree skeletons (a main trunk and basal part of first-order branches) extracted from terrestrial LiDAR data and some architectural rules to add foliage to branches.

Fast automatic method for constructing topologically and geometrically precise tree models from TLS Data

Pasi Raumonen, Eric Casella, Mathias Disney, Markku Åkerblom, Mikko Kaasalainen — Mon, 03 Jun 2013 13:17:24 +0300

We present a computational method that produces automatically precision models of trees from terrestrial laser scanning (TLS) data. The method is fast, typically few minutes per tree, and the resulting model contains both the topological and geometrical information of the tree. The method is validated using artificial and real TLS data. The results show that TLS together with computational reconstruction method provides means to collect structural information of trees fast and nondestructively.

A geometrical model generator for quasi-axisymmetric fruit

Mon, 03 Jun 2013 13:19:21 +0300

A geometrical model generator for fruit is presented. The generator uses X-ray tomography images of quasi-axisymmetric fruit as input, describes the shape of the fruit with elliptical Fourier descriptors, and uses statistical analysis to randomly generate new representative fruit shapes from this dataset, which can be directly used as CAD models for CFD or FEM analysis.

Automatic 3D plant reconstruction from photographies, segmentation and classification of leaves and internodes using clustering

Thiago Teixeira Santos, Julio Akira Ueda — Mon, 03 Jun 2013 13:21:15 +0300

A stereo approach for 3D plant modelling is presented. Using only a set of photographies, the method produces a dense 3D point cloud sampling the plant surface. Clustering automatically segments the plant structure in meaningful parts, which are classified in elements of interest as leaves and internodes. Measurements can be computed for each element, as area or surface normals.

Monitoring the diel growth of individual Arabidopsis leaves using a laser scanning approach

Tino Dornbusch, Olivier Michaud, Christian Fankhauser — Mon, 03 Jun 2013 13:23:09 +0300

A novel phenotyping approach is presented to monitor diel variation in elongation and elevation angle of individual leaves with high precision and throughput. Leaf elongation and changes in leaf elevation angle follow characteristic diel rhythms and show an overall decrease with increasing leaf age.

A Blender addon for the 3-d digitizer FASTRAK for plant structure acquisition

Mon, 03 Jun 2013 13:24:28 +0300

An addon for the open-source 3-d graphical modelling software Blender was implemented. It enables communication with the electromagnetic 3-d digitizer FASTRAK via a serial interface. Discrete and continuous point acquisition mode, immediate visualization in Blender's 3-d view, acoustic feedback, creation of standard geometry (e.g., cylindrical internodes) and of free-form volumetric shapes (for fruits, tree trunks etc.), calibration and rectification in case of field disturbances, and MTG export are supported.

KEYNOTE: Interplay between material flows and structural properties in dynamics of tree growth

Teemu Hölttä, Eero Nikinmaa — Mon, 03 Jun 2013 15:05:18 +0300

A whole tree level theoretical framework on the linkage between leaf gas exchange, long distance xylem and phloem transport and tree growth is presented.

Transpiration from stomata via the leaf boundary layer: a microscale modelling approach

Thijs Defraeye, Pieter Verboven, Jan Carmeliet, Dominique Derome, Bart Nicolai — Mon, 03 Jun 2013 15:07:16 +0300

Convective mass transport from entire leaf surfaces was investigated with computational fluid dynamics. A novel aspect is that the stomata were modelled discretely. The convective exchange rate was relatively large, even for the limited surface coverage by stomata, and had a complex dependency on surface coverage and air speed. In addition, insight in the boundary-layer transfer at microscale level was obtained.

LEAFC3-N: Modeling Effects of Drought Stress on Photosynthesis, Stomatal Conductance and Transpiration

Jens Bastet, Johannes Müller, Olaf Christen — Mon, 03 Jun 2013 15:16:58 +0300

LEAFC3-N combines photosynthesis, stomatal conductance, transpiration, leaf energy balance, and leaf nitrogen content. The response to drought is simulated accounting for the effect of leaf water potential on stomatal conductance and of a finite mesophyll conductance on intracellular CO₂ concentration.

Modelling transport processes in tissues and organs at a mesoscopic scale

Ansgar Bohmann, Juliane Claus, Andrés Chavarría-Krauser — Mon, 03 Jun 2013 15:30:02 +0300

Three mesoscopic models of transport processes in plants are presented: water fluxes in tissues, zinc uptake in roots, and gas fluxes in leaves. The models aim at increasing our understanding of the interaction between physical and biological processes in plants. Besides giving ideas for derivation of other mesoscopic models, the presented results can be of use in functional-structural plant models.

Spatial and temporal variability of leaf gas exchanges and temperature responses to drought on apple trees assessed by a 3D turbid medium model

Jerome Ngao, Boris Adam, Marie Charreyron, Marc Saudreau — Mon, 03 Jun 2013 15:32:29 +0300

Drought stress alters tree carbon and water balance, and it could affect pest and disease development as affected by changes in microclimate. Spatial and temporal variability of leaf gas exchange and microclimate (through leaf temperature) were assessed by adapting a 3D turbid medium model to drought stress and comparing model outputs to drought experiments.

Dynamic properties of foliage photosynthesis

Edward David Ford, Shawn Behling — Mon, 03 Jun 2013 15:33:28 +0300

Increasing results illustrate the importance of modelling photosynthesis as a dynamic process where the parameters of the standard photosynthesis curve vary in response to fluctuations in environmental conditions and developmental status of the plant. We describe how engineering approaches to the analysis of dynamic systems can be used and provide information for incorporating the dynamics of photosynthesis into large scale FSPMs.

Revealing the relative importance of photosynthetic limitations in cucumber canopy

Mon, 03 Jun 2013 15:34:42 +0300

We identified that in a two meter high greenhouse grown cucumber canopy, photosynthesis is mostly light-limited, and light interception and biochemical capacity are the major factors limiting photosynthesis. The diffusion pathways, stomatal and mesophyll conductance, are minor restrictions.

Integrating architecture and physiological perspectives in fruit development

Mon, 03 Jun 2013 15:36:40 +0300

Architectural properties of a fruit, such as its shape, vascular patterns, and skin morphology, play a significant role in determining the distributions of water, carbohydrates, and nutrients inside the fruit. Understanding the impact of these properties on fruit quality is difficult, because they develop over time and are highly dependent on both genetic and environmental controls. We developed a 3D fruit model that can be used to investigate effects of the principle architectural properties on fruit quality.

Up-scaling salt effects in cucumber: trade-off between photosynthesis and toxic ion accumulation

Tsu-Wei Chen, Katrin Kahlen, Hartmut Stützel — Mon, 03 Jun 2013 15:37:54 +0300

A dynamic cucumber FSPM, describing the effects of salinity on the plant morphology and the pattern of sodium accumulation in leaves, is parameterized and evaluated. This model is a first step in exploring mechanisms which improve plant tolerance and WUE at canopy level under salinity stress.

A model of mechanics and gas exchange in a neighborhood of a single stoma

Ansgar Bohmann, Andres Chavarria-Krauser — Mon, 03 Jun 2013 15:53:58 +0300

The interplay of stomatal behaviour, epidermis mechanics, water flow, and diffusion is modeled dynamically with a system of ordinary and partial differential equations based on mechanical and thermodynamic principles. Simulation results of the discretised equations are shown.

A mechanistic model for the estimation of the quantum yield of photochemistry based on light, temperature, and chlorophyll a fluorescence

Beñat Olascoaga, Albert Porcar-Castell — Mon, 03 Jun 2013 15:55:15 +0300

By studying chlorophyll a fluorescence emissions from a range of light intensities in Scots pine saplings acclimated to different temperatures, we aim to build a model to interpret chlorophyll a fluorescence capable of estimating the quantum yield of photochemistry.

Simulated interaction between tree structure and xylem and phloem transport in 3D tree crowns using model LIGNUM

Eero Nikinmaa, Risto Sievänen, Jari Perttunen, Teemu Hölttä — Mon, 03 Jun 2013 15:56:48 +0300

We have implemented xylem and phloem transport model (Hölttä et al. 2006) with 3D tree model LIGNUM to study how structural traits in tree crown influence the transport in branched architecture with observed transpiration and photosynthetic response to driving environmental variables. We study how structural traits in tree crown influence the xylem and phloem transport and associated pressure gradients when observed transpiration and photosynthetic response to driving environmental variables are applied in branched architecture.

Integrating water transport into L-kiwi model using an aspect-oriented approach

Helge Dzierzon, Alla N. Seleznyova — Mon, 03 Jun 2013 15:58:06 +0300

A simple as well as transparent soil-vine water transport model was created and integrated into the functional model L-kiwi using L-Systems and the aspect-oriented approach. The model will play an important part in modelling variability of the fruit quality within the vine canopy.

Integration of a mechanistic biochemical and biophysical leaf gas exchange model in L-PEACH

Inigo Auzmendi, Romeo Favreau, David Da Silva, Theodore DeJong — Mon, 03 Jun 2013 16:00:41 +0300

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Towards integrating primary C-N metabolism and physiology of crop growth across different plant scales: the ProNet-CN model – a multiscale approach

Johannes Müller, Andre Eschenröder, Olaf Christen — Mon, 03 Jun 2013 16:01:57 +0300

ProNet-CN is a new multiscale process network integrating biophysical, metabolic, and physiological processes of biomass formation across plant scales. It combines the LEAFC3-N model describing the exchange of CO₂, water vapor, and energy with a new model of the dynamics of mass balances of main carbon and nitrogen metabolites and its allocation between interacting compartments or organs.

Modelling zinc uptake and radial transport in roots

Juliane Claus, Ansgar Bohmann, Andrés Chavarría-Krauser — Mon, 03 Jun 2013 16:03:53 +0300

Modelling of zinc radial transport in roots was undertaken to understand the experimentally observed pattern of zinc accumulation near the central cylinder of the root. The model confirms the hypothesis that low abundance of the efflux transporter HMA4 produces this radial gradient in zinc concentration, but surprisingly, transpiration was found also to be a key parameter.

Simulating the impact of (“long-distance” or “root-to-shoot”) hormonal signaling and non-uniform soil water distribution on plant transpiration

Mon, 03 Jun 2013 16:05:06 +0300

In response to non-uniformly distributed soil water, root water uptake and actual (whole plant) transpiration was simulated using R-SWMS as part of the soil dried. These variables varied widely (reduction between 10 and 55 percent) between plants with different controls of stomatal conductance, i.e. controlled by leaf water potential and/or by the concentration of a hormonal signal triggered by low root water potentials in dry soil regions. Hormonal regulation of transpiration was effective only for a limited time, when water flow out of drying soil regions was sufficient to transport hormones to the shoot.

Modelling Spatial and Temporal Leaf Temperature Dynamics - A focus on the leaf boundary layer

Marc Saudreau, Boris Adam, Amélie Ezanic, Sylvain Pincebourde — Mon, 03 Jun 2013 16:06:19 +0300

A 3D leaf temperature model is proposed to estimate dynamics of temperature gradients at leaf surface. The 3D leaf shape, the leaf physiology, and the microclimate are accounted for. CFD was used to prescribe realistic spatial evolution of the sensible heat flux at the leaf surface.

Hydraulic constraints influence the distribution of canopy photosynthetic properties

Mikko Peltoniemi, Remko Duursma, Belinda Medlyn — Mon, 03 Jun 2013 16:11:24 +0300

We showed that limited water transport capacity to upper canopy leaves leads to sub-optimal photosynthetic performance of a tree. In these cases, the widely applied assumption of optimal N distribution that follows irradiance distribution does not hold. Hydraulically constrained optimum N distribution would be flatter than the distribution of irradiance. We further showed that in order to maximize canopy photosynthesis, trees should allocate water transport capacity and N co-optimally, which means allocating both of them according to irradiance distribution.

Reliable estimation of parameters of the Farquhar-Von Caemmer-Berry Biochemical model cannot be obtained by fitting An/Ci curves

Mon, 03 Jun 2013 16:13:26 +0300

Because of the limited accuracy of datasets and limited number of data points of each dataset, the parameters of the Farquhar-von Caemmerer-Berry photosynthesis model cannot be reliably estimated by analysis of A_n/C_i datasets with the same accuracy of the data measured from currently available commercial gas exhange device.However , the resulting fitted parameter set by methods of Sharkey et al. (2007) and Gu et al. (2010) remains useful to predict photosynthesis.

Stem diameter variation: endogenous regulation versus environmental dynamics and its implication for functional modelling

Maurits Willem Vandegehuchte, Adrien Guyot, David Lockington, Kathy Steppe — Tue, 04 Jun 2013 10:30:59 +0300

Stem diameter variations are generally modelled based on the time lag between transpiration and root water uptake. However, small differences in endogenous osmotic regulation of the storage tissue can result in significant changes in stem diameter variation. This endogenous control needs to be taken into account in functional-structural plant models to accurately predict growth.

Crop load effects on stem diameter variations in peach evaluated with an integrated plant and fruit model

Tue, 04 Jun 2013 10:32:04 +0300

Integrating a mechanistic carbon and water flow model with a model of peach fruit water and carbon accumulation enabled to quantify plant carbon relations with varying crop load. Physiological processes at the plant level could as such be related to effects on fruit growth.

Physiological growth model CASSIA predicts carbon allocation and wood formation of Scots pine

Tue, 04 Jun 2013 10:33:08 +0300

The dynamic, intra-annual model CASSIA combines detailed models of wood formation and properties with a process-based growth simulation system. It predicts the daily growth of wood, needles, shoots and roots of Scots pine based on weather variation and photosynthetic production.

Understanding and evaluating some allometric relationships useful for functional-structural plant modeling.

María Paulina Fernández — Tue, 04 Jun 2013 10:34:49 +0300

The dynamic process of development and growth of Pinus radiata trees was studied during an entire growing season and the allometric relationship between foliage biomass and the supporting conductive area of tissues analyzed. Changes in the stem through time of this relationship suggest that the use of a constant and fixed value for modeling purposes leads to wrong results. This subject is discussed and illustrated by means of simulations.

What are the processes driving carbon allocation to stem and fine roots in a mature coppice of Quercus ilex in the Mediterranean? A data model analysis

Tue, 04 Jun 2013 10:36:55 +0300

Improving carbon allocation in process based model is a challenging issue. A process model was prescribed using an extensive data set of growth and carbon fluxes (11 years) at the stand scale in order to draw new carbon allocation scheme in Q. ilex. Our results suggest that a part of summer photosynthesis is used for the renewal of fine roots.

Modelling temperature-modulated internode elongation in greenhouse grown cucumber canopies

Katrin Kahlen, Tsu-Wei Chen, Jana Zinkernagel, Hartmut Stuetzel — Tue, 04 Jun 2013 10:38:33 +0300

This study highlights the significance of temperature signals for predicting final internode length: Growth and appearance rates need to be adapted to the prevailing temperature conditions. Variations in the light environment additionally alter the pattern of final internode length along the main stem and thus indicate the importance of considering simultaneously acting factors.

Height increment formation of hybrid aspen: empirical model

Aris Jansons, Juris Rieksts Riekstins, Martins Zeps, Oskars Krisans — Tue, 04 Jun 2013 10:41:56 +0300

Model predicting height growth rate based on mean daily temperature was statistically significant (p < 0.01), both intercept and slope coefficient were significantly different from zero (p < 0.01) and determination coefficient high R²=0.83. Model predictions for height increment in next season did not differ significantly from the measurements. It can be used as part of the system for predictions of effect of global climatic changes on height growth in hybrid aspen plantations

Masting changes canopy structure, light interception, and photosynthesis in Fagus crenata

Atsuhiro Iio — Tue, 04 Jun 2013 10:42:42 +0300

Masting-dependent changes in canopy structure, light interception, and photosynthesis in natural Fagus crenata forests were examined with field-research and light transfer model. Masting significantly decreased canopy leaf area, especially in the upper layer, but increased whole canopy photosynthesis because of increased light interception in the lower layer. These masting-dependent changes are important for precise carbon budget estimation in forest ecosystems.

The effect of low phosphorus on morphological and physiological characters of gooseberry plants (Physalis peruviana)

Gabriel Roveda, L.P. Moreno-Fonseca — Tue, 04 Jun 2013 10:43:56 +0300

P-deficiency decreased total biomass and changed the dry matter distribution, the leaf numbers, the total leaf area, and the root length density, as consequence of the photosynthesis rate reduction. In addition, P-deficiency induced enhancement of antioxidant activity, CAT, POD, with a reduction of the total protein. There are evidences related to the damage of cell membranes by ROS.

A fifty-year-old conceptual plant dormancy model provides new insights into dynamic phenology modelling

Heikki Hänninen, Robin Lundell, Olavi Junttila — Tue, 04 Jun 2013 10:44:41 +0300

Vegis’ (1964) conceptual plant dormancy model has been largely ignored in dynamic models of growth onset phenology. We formulate a dynamic model including the phenomenon assumed in the conceptual model and show that the phenomenon 1) potentially explains previous contradictory results of model testing and 2) is crucial with respect to the effects of climate warming on boreal trees.

A single tree basal area growth model

Jan Hoogesteger — Tue, 04 Jun 2013 10:45:29 +0300

What is the role of the structural and circular constraints on tree growth dynamics? Simple rules about growth and self-pruning result in a 2-dimensional dynamic growth model in a framework of structural and circular constraints. The results suggest that onset and rate of self-pruning are key factors in the partitioning of dry matter between foliage and wood.

Towards a FSPM of bud outgrowth for rosebush: experimental analysis of sugar effect.

Tue, 04 Jun 2013 10:46:19 +0300

This study provides experimental data on rosebush to extend the auxin-based FSPM model of bud outgrowth to account for sugar roles. The analysis of the relationship between sugar availability and bud outgrowth at both plant and bud scales showed that sugar availability is able to decrease apical dominance by reducing the lag time before bud outgrowth.

Geometrically saturated growth and the pipe model of tree form

Lars Hellström, Linus Carlsson, Åke Brännström — Tue, 04 Jun 2013 10:46:56 +0300

We combine our self-thinning model of geometrically saturated growth with the pipe model of Shinozaki et al. to yield a composite model that can be used to make predictions about quantities traditionally found in functional models of tree growth.

Functional-structural modelling of tree and wood formation: new parameters and relations.

María Paulina Fernández, Iván Lillo — Tue, 04 Jun 2013 10:47:46 +0300

Foliage development and growth of Pinus radiata are modulated by temperature, water balance, and probably also by photoperiod, with marked tendency changes associated to solstices and equinoxes or at times close to them. Being a highly coordinated process, wood density of growing rings also vary, increasing or decreasing, according to current crown developmental trends. In addition, it appears that a constant thermal accumulation value triggers the formation of a new wood cell. A functional-structural model combines these phenomena and links new foliage development and expansion to wood formation and density.

Functional overwintering types as basis for modelling the overwintering of northern field layer plants under climate warming

Robin Lundell, Heikki Hänninen, Timo Saarinen, Helena Åström — Tue, 04 Jun 2013 10:48:39 +0300

Three overwintering types were identified among boreal field layer plants by using growth chamber experiments in combination with phenological dynamic models of the annual cycle. These types form the basis for modelling the responses of overwintering plants to climate change.

Patterns of carbon and nitrogen allocation in trees predicted by a model of optimal plant function

Ross Edward McMurtrie, Roderick C. Dewar — Tue, 04 Jun 2013 10:49:53 +0300

Annual carbon allocation to leaves, stems and roots of trees is predicted by a model that simulates canopy photosynthesis and root nitrogen uptake with the overlying hypothesis that annual wood production is maximised.

L-Rose: a model simulating organ expansion of individual plants within a rose bush crop

Tue, 04 Jun 2013 10:50:35 +0300

A model has been developed to simulate the dynamics of expansion of the individual organs of rose bush primary shoots. This model is designed to provide a tool calibrated on experimental data to investigate plant response to phylloclimate, especially light.

KEYNOTE: Biotic systems as multilevel dynamic information processing ssys

Paulien Hogeweg — Tue, 04 Jun 2013 12:19:33 +0300

Multilevel modeling may simplify the modeling of complex biological processes.

Integrating multiple scale dynamics: Application to Fagus sylvatica under ozone exposure

Yongzhi Ong, Katarína Smoleňová, Michael Henke, Winfried Kurth — Tue, 04 Jun 2013 12:21:11 +0300

An integrated dynamic model of ozone concentration trends, stand dynamics, radiation interception, structural growth, functional systems and molecular pathways is constructed for beech trees. The model composes incomparable spatial decompositions and functional processes in a single graph-based framework. Extensions to the programming language XL for multi-scale rule-based modeling are applied in order to gain insights into the challenges that scale integration poses on language formalisms.

Simulating the evolution of optimal rooting strategies in shallow soils and extreme climates

Michael Renton, Pieter Poot — Tue, 04 Jun 2013 12:22:07 +0300

Functional-structural models of root development combined with evolutionary optimisation algorithms can provide insights into why plant species develop different strategies in different environments and conditions.

AMAPstudio: a 3D Interactive Software Suite for Plants Architecture Modelling

Sébastien Griffon, François de Coligny — Tue, 04 Jun 2013 12:23:28 +0300

Plants architecture modelling results in building complex models. Turning them into simulators requires strong interaction between scientists and software developers. The AMAPstudio project adapts a methodology that has been successfully conducted in the forestry modelling field for 12 years. It focuses on a long-term supported software environment and a strong customized technical backing to help modellers integrate their simulators in highly 3D interactive software.

Modelling Competition in Crop Populations via Reaction-Diffusion Foliage Dynamics. With an Outlook on Tree Modelling

Robert Beyer, Paul-Henry Cournède — Tue, 04 Jun 2013 12:24:21 +0300

Local leaf area index is considered as a spatially continuous variable, subject to dynamics of allocation, senescence and spatial propagation. This approach allows for inter-individual variability and competition while maintaining robustness – a key shortcoming of comparable models. Simulation results inspire a three-dimensional generalisation towards trees, alongside which an underlying dynamic branch system is devised, targeting finer morphological accuracy.

Improving finite element models of roots-soil mechanical interactions

Ming Yang, Pauline Défossez, Thierry Fourcaud — Tue, 04 Jun 2013 12:26:07 +0300

Finite element models (fem) of roots-soil mechanical interactions have been tested taking into consideration different levels of simplifications, i.e. considering the discretization of roots with solid elements and root-soil contact behaviour, and structural beam elements embedded in the soil matrix respectively. These two modelling options have been tested and compared simulating direct shear tests of reinforced soils. The “frictional behaviour” method used with solid elements predicted shear strength of the root-soil system 4.6-6.9% higher than that predicted with “embedded beam elements”. This difference can be considered as negligible. Embedded beam elements were thus chosen to discretized digitized Maritime pine root systems and to test the effect of root failure on the mechanical response of trees to overturning.

Integrative models for analyzing jointly shoot growth and branching patterns

Tue, 04 Jun 2013 12:27:53 +0300

The branching pattern of a shoot may be influenced by numerous factors varying along the shoot such as the internode length, the leaf surface or the local curvature. We introduce a generalization of hidden semi-Markov chains for categorical response variables that incorporates explanatory variables varying with the index parameter. Using this model, we demonstrate the influence of the growth pattern of a shoot on its immediate branching.

Deciphering mango tree asynchronisms using Markov tree and probabilistic graphical models

Tue, 04 Jun 2013 12:29:30 +0300

Tree development is often characterised by complex dependencies between growth units (GUs) deriving from a given mother GU. We introduce a new methodology to identify such dependencies with parsimonious statistical models. The proposed approach is illustrated on mango tree, a tropical species with a particularly complex timing of development. We focus especially on asynchronism between sister GUs within tree architecture.

OpenAlea 2.0: Architecture of an integrated modeling environment on the web

Tue, 04 Jun 2013 12:47:53 +0300

Plant modeling is based on the use of a diverse set of design paradigms (L-systems, visual programming, imperative languages or sketch-based interfaces). In this poster, the architecture of a new multi-paradigm and integrated modeling environment is presented. This desktop application will become a distributed web application, allowing to run simulations on a cloud computing system and share virtual experiments on the web. The modeling environment will run on a web browser using HTML5 and WebGL technologies.

Rule-based integration of LIGNUM into GroIMP

Katarina Smolenova, Michael Henke, Yongzhi Ong, Winfried Kurth — Tue, 04 Jun 2013 12:48:41 +0300

LIGNUM is a functional-structural tree model combining the use of L-systems for structural development and a general-purpose programming language for modelling metabolic processes and radiation regimes. We show how both the structural and functional part of LIGNUM, used for a Scots pine model, can be translated into the rule-based language XL, thus offering new possibilities for model reuse and comparison.

An extension of the graph-grammar based simulator GroIMP for visual specification of plant models using components

Michael Henke, Katarína Smoleňová, Yongzhi Ong, Winfried Kurth — Tue, 04 Jun 2013 12:49:28 +0300

The FSPM platform GroIMP was extended by a graphical editor for components of rule-based models, enabling a better re-use and comparison of submodels. Components can be arbitrarily nested and can have several types of connectors with different semantics. The new tool provides a parallel maintenance of model code and of the graphical view showing the component structure.

Global sensitivity analysis of the NEMA model for its parameterization and biological diagnosis

Qiongli Wu, Jessica Bertheloot, Paul-Henry Cournède — Tue, 04 Jun 2013 12:52:59 +0300

A new comprehensive methodology of global sensitivity analysis is applied on NEMA model. Besides the common objectives of global sensitivity analysis for ranking the importance of individul input factors, we also anayzed specifically about function modules in the model, hence we can get the information about the improtance and interactions of the physical processes attached to these modules. The result can be very helpful in the parameterization process and provide new biological insights and diagnosis for NEMA.

Reconstruction of leaf area time series using data assimilation on the GreenLab plant growth model and remote sensing

Xing Gong, Thomas Corpetti, Mengzhen Kang, Baogang Hu, Laurence Hubert-Moy — Tue, 04 Jun 2013 12:54:56 +0300

The GreenLab plant growth model is a powerful and complex tool able to simulate plant growth evolution. The calibration of GreenLab model for a specific plant usually requires field experiments with destructive sampling periodically done on individual plants in order to characterize growth and organogenesis. However when one is merely interested on particular aspects of plant growth, such as leaf area evolution or fruit harvest, we demonstrate in our work that a substantially simplified GreenLab model, associated with data assimilation methods, is able to provide satisfactory performances. Based on these techniques, we have successfully applied GreenLab to remote-sensing area where the observation data is highly limited. Experimental results show that qualitative and quantitative criteria on leaf area reconstructed time series are of good quality.

KEYNOTE: A critical role for root models in feeding 10e10 people

Jonathan Lynch — Tue, 04 Jun 2013 13:00:35 +0300

There is an urgent need to develop crops with reduced nutrient and water requirements. The complexity of relevant processes overwhelms conventional empirical approaches. Structural-functional modeling of root systems has a unique role in providing important insights into the root phenome, which will focus empirical research on the most productive avenues, and inform crop ideotype development.

Integration of root system in a ryegrass perennial model based on self-regulation

Tue, 04 Jun 2013 13:02:46 +0300

An Individual-based functional-structural model of heterogeneous mini populations of ryegrass plants can be a useful tool to improve our understanding of the grassland use-value creation. Here we present the L-grass model that allows simulating the shoot and root development of plants with different morphologies using self-regulation rules in an auto-organized architectural system.

Modelling Sugar maple development along its whole ontogeny: modelling hypotheses and calibration methodology

Olivier Taugourdeau, S Delagrange, P de Reffye, C Messier — Tue, 04 Jun 2013 13:04:16 +0300

Relevant GreenLab model hypotheses can be used to model sugar maple development along its whole ontogeny. A dedicated methodology is presented for model calibration (from measurement to parameter calibration). It allows the modelling of long lived trees with highly complex structures.

Characterizing the balance between ontogeny and environmental constraints in forest tree development using growth phase duration distributions

Yann Guédon, Olivier Taugourdeau, Yves Caraglio, Sylvie Sabatier — Tue, 04 Jun 2013 13:06:28 +0300

We built segmentation models to identify tree growth phases on the basis of retrospective measurement of annual shoot characteristics along the main stem. Growth phase duration distributions estimated within these models characterize the balance between ontogeny and environmental constraints in tree development at the population scale. These distributions have very contrasted characteristics in terms of shape and relative dispersion between ontogeny-driven and environment-driven tree development.

Influence of canopy architecture and parameters of leaf level photosynthesis on dry matter production in greenhouse cucumber

Dirk Wiechers, Katrin Kahlen, Hartmut Stützel — Tue, 04 Jun 2013 13:09:42 +0300

Productivity of crops highly depends on structural and physiological parameters. Using a FSPM we analyzed the sensitivity of key parameters revealing the strong influence of structural differences as well as the dominant role of light and stomatal control on the physiological parameters.

Light signal perception in Arabidopsis rosettes

Jochem B Evers, Ronald Pierik, Alexander A R van der Krol — Tue, 04 Jun 2013 13:10:45 +0300

Light signals are important cues for future and current competition. We used an architectural model of Arabidopsis development to show that vertical growth of neighboring vegetation is more important than proximity for early detection of competition. Self-signaling is greatly enhanced when own organs grow more vertically, and signal strength differs between signal perception at the apex compared to the leaves.

How do variations of architectural parameters affect light partitioning within wheat-pea mixtures? A simulation study based on a virtual plant approach.

Tue, 04 Jun 2013 13:12:02 +0300

3D and dynamic models of wheat and pea were used to study light partitioning in virtual wheat-pea mixtures. Our results showed that architectural parameters defined at plant scale (e.g. branches, internode length) significantly affect the interception of light by each component species. The modifications performed on the architectural parameters of both models led to asymmetric variations of light partitioning.

Influence of the genetic variation of branching during early growth on light interception efficiency of apple trees: a modelling study with MAppleT

David Da Silva, Liqi Han, Robert Faivre, Evelyne Costes — Tue, 04 Jun 2013 13:13:26 +0300

Light interception is a key parameter to optimise fruit tree production. Assuming that genetic variability of branching along trunks impacts tree development, total leaf area and light interception in the consecutive years, we estimated STAR values on 1 to 5 years old simulated apple trees. We analyse the relative impact of proleptic and sylleptic shoots, and depending on their length category on STAR variance

Quantitative characterization of clumping in Scots pine crowns

Pauline Stenberg, Matti Mõttus, Miina Rautiainen, Risto Sievänen — Tue, 04 Jun 2013 13:15:16 +0300

The stochastic approach of modeling tree crowns as geometric shapes filled with a random medium was tested on twelve Scots pine trees generated with the LIGNUM model. Results supported the capability of the stochastic approach in characterizing clumping in crowns given that the outer shell of the tree crown is well represented.

Towards three-dimensional modeling light capture of crop canopy considering regional variation of incident radiation

Tongyu Hou, Tao Duan, Zhaoli Xu, Yuntao Ma, Bangyou Zheng, Yuhong Yang, Yan Guo — Tue, 04 Jun 2013 13:16:53 +0300

A GIS-based model was adopted to simulate the regional variation of incident photosynthetically active radiation (PAR) in mountainous area. The PAR capture of rice and tobacco canopies at four special eco-sites was calculated utilizing three-dimensional modeling. This provides the basis for using functional-structural models to simulate crop growth and assess plant types at different regions accurately.

Modeling Seasonal Patterns of Carbohydrate Storage and Mobilization in Peach Trees

David Da Silva, Liangchun Qin, Carolyn Debuse, Theodore DeJong — Tue, 04 Jun 2013 13:18:27 +0300

Storage of carbohydrate is essential for perennial plants survival, but its modeling is often unsatisfactory. We studied the dynamics of reserve storage and mobilization in Peach trees and introduced a modeling approach that consider storage as an active sink rather than a passive buffer as frequently done in carbon-based models of tree growth.

Simulation of small footprint full waveform LiDAR signals from seedling stand vegetation using Monte Carlo ray tracing and statistical models of 3D vegetation structure

Aarne Hovi, Ilkka Korpela — Tue, 04 Jun 2013 13:30:55 +0300

A Monte Carlo ray tracing model for simulation of waveform recording LiDAR data was developed. Species-specific waveform characteristics in real data were accuratelyreproduced in simulations. The model was used to study the effects of sensorparameters on vegetation classification performance. Effect of LiDAR footprint could be shown.

Between- and within-tree shading in mixed stands: shoot-level simulation

Anna Lintunen, Pekka Kaitaniemi, Jari Perttunen, Risto Sievänen — Tue, 04 Jun 2013 13:32:47 +0300

Between- and within-tree light transmission is simulated with ray casting method in reconstructed mixed stands consisting of Scots pine and silver birch.

A modeling approach to simulate the whole-plant leaf expansion responses to light in three annual dicotyledonous species

Tue, 04 Jun 2013 13:34:36 +0300

A generic leaf area growth model based on the simulation of leaf growth dynamics in response to light microclimate was built, calibrated and validated for three dicotyledonous species.

Characterization of the relationship between quantity and quality of solar radiation in canopy under contrasting sky conditions

Cailian Lao, Zhaoli Xu, Yan Guo, Yan Jin, Yuhong Yang — Tue, 04 Jun 2013 13:36:14 +0300

Spatial radiation distribution in tobacco canopy was measured and analyzed according to spectral composition under clear and overcast sky conditions.

Artificial neural networks in modeling of environmental time series for yerba-mate growth dynamics

Fabio Takeshi Matsunaga, Miroslava Rakocevic, Jacques Duílio Brancher — Tue, 04 Jun 2013 13:38:06 +0300

The artificial neural networks (ANN) are a solution to model the nonlinear systems. The monthly mean values of environmental and morphological data were used to build time series related to yerba-mate growth. Time series and data relative to rhythmic growth were used for ANN training. The final results of this FSPM are yerba-mate mock-ups, related to two particular environmental conditions.

Building the foundations of a Coffea arabica FSPM

Tue, 04 Jun 2013 13:41:52 +0300

Several data sets are being gathered to build a functional-structural model for Coffea arabica. The one pitfall in this integration process is the difficulty of calibrating a large number of parameters. A step by step procedure is thus necessary to validate the sub-models. The focus is put here on the backward reconstruction of the plant structure from its description at a given time as a way to decrease the degrees of freedom of the model before addressing the carbon acquisition and allocation.

Evaluation of a photon tracing model and virtual plants to simulate light distribution within a canopy in a growth chamber

Tue, 04 Jun 2013 13:44:04 +0300

Radiance distribution in a growth chamber is anisotropic. Our objective is to evaluate the accuracy of light simulations in a rose canopy grown in a growth chamber using virtual plants and a photon tracing model dedicated to growth chambers. The question of the scale at which the system reproduces the observed variability is specifically addressed.

Simulating maize plasticity in leaf appearance and size using regulation rules

Tue, 04 Jun 2013 13:45:28 +0300

Plant regulate their architecture in response to growth environment, which challenges us to design models capable of performing well in different conditions. By using self-regulating rules, we reproduced blade and collar emergence time, and organ size distribution along phytomer rank in maize under varying growing conditions. The role of emergence events, e.g. blade tip emergence, collar emergence, in controlling growth stage and elongation duration of different components of one phytomer (blade, sheath and internode) are confirmed.

How petiole flexibility changes light interception at the tree scale.

Loïc Nabil Tadrist, Emmanuel de Langre, Marc Saudreau — Tue, 04 Jun 2013 13:46:41 +0300

Leaf inclination angle plays a key role for light interception of a tree. However existing models for this quantity are empirical, not predictive and do not take into account the fact that leaves are flexible. Based on a leaf mechanical model and a multi-scale approach we propose a model of leaf inclination angle distribution and quantify how much leaf flexibility may change light interception of a tree.

Concept and Calibration of Virtual Wheat Including Stochastic Tillering

Lu Feng, Hervé Rey, Jean-Claude Mailhol, Mengzhen Kang, Philippe de Reffye — Tue, 04 Jun 2013 13:48:27 +0300

Present study has introduced a comprehensive theoretical architecture to note probability of phytomer occurrence to describe wheat structural development. This provided an intermediary to compute the overall level of growth functions. The model then was calibrated on observation of variform individuals.

The effect of canopy structure on photochemical reflectance signal

Matti Mõttus, Miina Rautiainen — Tue, 04 Jun 2013 13:50:05 +0300

We measured the angular distribution of spectral scattering properties of Scots pine shoots. We were able to scale the photochemical reflectance index (PRI) between two canopy structural levels using photon recollision probability. We found non-negligible anisotropy in shoot PRI possibly caused by reflectance of the needle wax coating.

A geometric model for scaling between needle and shoot spectral albedos

Tue, 04 Jun 2013 13:51:14 +0300

The spherically averaged shoot silhouette to total needle area ratio (STAR) can be used as a scaling parameter to link needle- and shoot-level spectral albedos in coniferous canopies.

Protocol for foliage modeling and light partitioning in Coffea arabica

Tue, 04 Jun 2013 14:14:39 +0300

Virtual coffee trees were reconstructed using partial morphological data, newly developed modules, AmostraCafe3D and VirtualCafe3D, and VPlants software. Leaf area size, STAR and transmitted PAR in different horizontal layers were computed on the virtual coffee plants and confronted to measurements.

A self-organising model of Macadamia with application to pruning in orchards

Neil Andrew White, Jim Hanan — Tue, 04 Jun 2013 13:54:56 +0300

A self-organising model of a macadamia that responds to pruning was created using the L-system-based language Lpfg. QuasiMC was used to determine light distribution within the canopy and reaching the orchard floor. Macadamia is an evergreen sub-tropical tree in the family Proteaceae and presents modelling challenges because of the abundance of leaves and multiple axillary buds.

Simulating the effect of extreme climatic events on tree architecture with a minimal FSPM

Olivier Taugourdeau, Jean-Francois Barczi — Tue, 04 Jun 2013 13:57:10 +0300

Tree response to extreme climate events is a hot topic considering climate change. Minimal mathematical modelling of interaction between tree growth and climate variation may help better understanding trees strategy to face extreme climate events.

Testing a radiation transmission model for stands consisting of individual 3D Scots pine and silver birch trees

Pekka Kaitaniemi, Risto Sievänen, Anna Lintunen, Jari Perttunen — Tue, 04 Jun 2013 13:59:54 +0300

Model-based estimation of light transmission showed acceptable precision in stands, which were reconstructed in 3D using basic tree-level forest inventory variables as input. It appears possible to limit the time costs of computation by restricting the number of sky sectors for ray tracing of light in the model.

Variation in structural and optical properties of sun exposed and shaded leaves: A model based approach

Petr Lukeš, Pauline Stenberg, Miina Rautiainen, Matti Mõttus, Kalle M. Vanhatalo — Tue, 04 Jun 2013 14:01:04 +0300

A database of optical, structural and biochemical properties of leaves of boreal species was established. The database was used to validate simulations of leaf spectra with the PROSPECT model. The relationships between leaf spectra and structure were similar for all species but the strongest for birch. The spectra of coniferous needles were more dependent on canopy position than birch spectra.

Influence of Morphological Traits on Wood Litter Production

Raffaele Rani, Konrad Abramowicz, Åke Brännström, Daniel Falster — Tue, 04 Jun 2013 14:02:27 +0300

We study the effect of variation of morphological traits on the wood litter production using an L-systems based model.

L-Pea: an architectural model of pea (Pisum sativum) development

Romain Barillot, Pierre Huynh, Abraham J Escobar-Gutiérrez, Didier Combes — Tue, 04 Jun 2013 14:03:24 +0300

An architectural model of pea, called L-Pea, was developped based on the L-System formalism. The input data account for the development of branches and phytomers as well as the kinetics of the vegetative organs growth.

Modeled and measured fPAR in a boreal forest

Titta Majasalmi, Miina Rautiainen, Pauline Stenberg — Tue, 04 Jun 2013 14:04:25 +0300

A new model was developed for the estimation of fPAR based on the spectral invariants theory. Good agreement was found between modeled and measured fPAR in boreal forests. The model was applied to study the effect of canopy structure and sky conditions on fPAR.

Real-time calculation of total light interception in crop canopy

Weiliang Wen, Xinyu Guo, Boxiang Xiao, Shenglian Lu — Tue, 04 Jun 2013 14:06:04 +0300

Daily total PAR interception is divided into three scales: organ, plant and canopy, and the core is organ scale calculation. Calculation of total intercepted PAR could be combined with photosynthetic rate parameter to study the relation between photosynthesis efficiency and production of specified canopy, after that, further analysis of agricultural production decisions may be carried out.

Plant structure in crop production: considerations on application of FSPM

Jan Vos, Jochem Bas Evers — Tue, 04 Jun 2013 14:29:14 +0300

Cereals, potato and glasshouse cut rose, representing monocot annuals, vegetative propagated dicot annual and woody perennials, have different structural development. ‘Bud break’, initiating tillering (monocots) and branching (dicots) is a key process determining plant structure. Plant population density is affecting bud break in each of these three species. The mechanisms explaining these observations and the application in models will be discussed, primarily carbon source : sink ratio and light quality (i.e. red : far red ratio.

Reparametrisation of Adel-wheat allows reducing the experimental effort to simulate the 3D development of winter wheat

Tue, 04 Jun 2013 14:30:42 +0300

A parameterization for dynamics of wheat plant architecture was developed with both high flexibility to adapt to contrasted genotypes and growth conditions and a reasonably low number of parameters, so that field measurements at 4-5 dates provide infromation required to simulate the whole crop cycle from seed emergence to grain maturity. Changes in leaf angles according to leaf age were shown to impact strongly ground cover. Simulations of ground cover and GAI matched field measurements all over the crop cycle.

Perspectives for improving carbon and nitrogen allocation in forest models from stand to global scale

Oskar Franklin, Peter M. van Bodegom — Tue, 04 Jun 2013 14:32:18 +0300

We show that using a fixed foliage: fine-root ratio leads to unrealistic modeled responses of forest growth to environmental variability (in particular to soil nitrogen availability). Not only the relative growth of organs (carbon allocation) will be off but also gross primary productivity predictions indirectly suffer from a lack of allocation flexibility. We suggest that applying evolution-based optimization principles to account for allocation plasticity is a key measure to improving future forest models and dynamic global vegetation models (DGVMs).

Photosynthesis, Transpiration and LAI: scale effects of spatial patterns

Moritz Kupisch, Anja Stadler, Matthias Langensiepen, Frank Ewert — Tue, 04 Jun 2013 14:35:18 +0300

Field level fluxes of CO₂ and H₂O as well as LAI are highly dependent on the underlying spatio-temporal patterns of environmental factors. Process models at the field scale have to consider the interaction with distribution and spatial patterns of input parameters applied on different plant response processes at the underlying leaf- and canopy-level.

Plant diversity and drought

Tue, 04 Jun 2013 14:37:17 +0300

We find a phase transition from no species to a highly diverse community, as the drought mortality and water table sharpness increases, but this is not true for water table depth. The species richness is decreasing with drought mortality and water table depth, but not with water table sharpness. Thin crown and intermediate values of photosyntetic efficiency (i. e. productivity) has the highest diversity.

Quantifying the potential yield benefit of root traits in a target population of environments

Mathieu Veyradier, John (Jack) T Christopher, Karine Chenu — Tue, 04 Jun 2013 14:47:20 +0300

Despite their importance, roots characteristics and their influence on crop growth remain poorly understood. A modelling approach was used to evaluate the potential impact of different root traits in targeted environments. Increased root extractable water at depth gave some substantial advantage to crops in all regions of the Australian wheatbelt, while increased root growth rate was only advantageous in the West of the belt.

X-Palm, a functional structural plant model for analysing temporal, genotypic and inter-tree variability of oil palm growth and yield

Tue, 04 Jun 2013 14:48:59 +0300

Oil palm yield depends on many component traits that are determined during about 4 years between inflorescence meristem initiation and harvest. Yield also presents large inter-month variability as well as variability among trees in the field. To simulate this complex system we developed a plant growth model using i) plant source-sink relationships as drivers of plant phenotypic plasticity and ii) stochastic rules relating inflorescence characteristics to plant nutritional status.

Modeling forest stand structure within a process-based model

Tue, 04 Jun 2013 14:50:26 +0300

A new empirical between-tree interaction module was implemented in the CASTANEA process-based forest stand model. The resulting functional-structural plant model demonstrates its ability to predict the morphological trajectories of individual trees grown in contrasted site conditions. The presented stand structure modeling can be profitably used to investigate forest responses to global changes and to design new silvicultural guidelines.

Effects of defoliation intensity on the genetic and phenotypic composition of virtual ray-grass populations

Tue, 04 Jun 2013 15:09:15 +0300

Successive generations of ray-grass plant populations were generated using the L-Grass FSPM model coupled with a simple genetic model. Results were compared to an experimental population. The first preliminary results show a weak modification of the genetic and phenotypic composition of the population between generations as a result of an increased defoliation intensity.

Formation of crown structure in Scots pine trees

Kourosh Kabiri, Eero Nikinmaa, Pertti Hari — Tue, 04 Jun 2013 15:10:12 +0300

The ecosystem model MicroForest describes the development of trees, ground vegetation and forest soil in a Scots pine stand based on coupling carbon and nitrogen fluxes in the system. Here, we simulated the crown development in a mature Scots pine stand assuming the semi-autonomous behaviour of the branches with optimizing C and N allocation simultaneously.

FSM-Rice: a simulation study on rice morphology using functional–structural plant modeling

Liang Tang, LeiLei Liu, Yonghui Zhang, Dongxiang Gu, Weixing Cao, Yan Zhu — Tue, 04 Jun 2013 15:11:04 +0300

A functional-structural plant model for rice (FSM-Rice) was developed by linking an existing rice growth model (RiceGrow) with a detailed morphological model (RiceArch) to realize dynamic visualization of 3D rice plant at organ, individual and population scales under different growth conditions and cultivars.

Parameterisation and evaluation of stand level process-based PipeQual-model for Norway spruce

Tuomo Kalliokoski, Harri Mäkinen, Annikki Mäkelä — Tue, 04 Jun 2013 15:12:07 +0300

We evaluated the process-based stand growth mode, PipeQual, with the data from the long-term experiments. Slope values between observations and simulations ranged from 0.96 to 1.05 depending on the variable illustrating the applicability of PipeQual for predicting forest stand growth in the future climate.

The model of root spreading and belowground competition in boreal mixed forests

Tue, 04 Jun 2013 15:13:01 +0300

New model of belowground competition is proposed. The model is operating on simulation grid and can simulate growth of root systems in mixed stands taking into account the irregularity in horizontal and vertical distribution of roots’ biomass. The main outputs are the density of roots in each cell and amount of nutrients captured by each tree.

Analysis of hybrid vigor for cucumber with Functional-Structural model Greenlab

Xiujuan Wang, Mengzhen Kang, Lili Yang, Baogui Zhang, Philippe de Reffye — Tue, 04 Jun 2013 15:14:20 +0300

To analyze the hybrid vigor between parent and hybrid plants, three cucumber cultivars were used (Parents: A, B; F1 hybrid: C). Detailed observations were performed using the continuous observations and destructive sampling during the growth of plants. Experimental results indicate that cyclic changes occur for the dry weight of organs (internode, leaf and petiole) of different positions during the stem. The yield, organ sizes and fruit number of the three cultivars were different. To analyze these differences, a Functional-structural model ’Greenlab’ was applied to compute the parameters of source sink for organs. The results demonstrate that plant architecture plays an important role on the heterosis breeding. This study is a first step to build a tool to provide the guidance of heterosis breeding for breeders on cucumber.

“Virtual grassland”: an OpenAlea package to deal with herbaceous plant architecture and grassland community dynamics

Gaëtan Louarn, Abraham Escobar-Guttierrez, Didier Combes — Tue, 04 Jun 2013 15:15:07 +0300

The “Virtual grassland” OpenAlea package was developed to provide herbaceous plant models and coupling methods with soil and light transfer modules. It aims at simulating the effects of competition and facilitation interactions at the population and community levels in grasslands.

A generic model of interactions between FSPM, foliar pathogens and microclimate

Tue, 04 Jun 2013 15:19:18 +0300

This study provides a framework based on a generic model of interactions between FSPM, foliar fungal pathogens and microclimate, with the concern of interoperability of the components and extensibility. The framework was applied to two disease models (powdery mildew on grapevine and septoria on wheat) previously developed on the platform OpenAlea, making them more modular and extensible. These improvements should enhance and ease the design of new disease models on FSPMs.

Using 3D virtual plants to evaluate the canopy role in the progression of a splash-dispersed crop disease: a case study based on wheat cultivar mixtures

Tue, 04 Jun 2013 15:25:44 +0300

A model taking into account physical mechanisms involved in splash dispersal of pathogens and host cultivar quantitative resistance has been developed to study the potential of heterogeneous three-dimensional crop canopies such as cultivar mixtures to prevent disease progression. We investigated different spatial organizations, proportions and resistance levels of wheat cultivars mixtures to allow better control of septoria tritici blotch

An integrated and modular model for simulating and evaluating how canopy architecture can help reduce fungicide applications

Tue, 04 Jun 2013 15:26:40 +0300

An integrated model coupling architectural canopy development, disease dynamics, pesticide application, pesticide decay and effect of pesticide on disease dynamics has been developed. It allows simulation of the dynamics of an epidemics overall a growth season, together with the evaluation of impacts on environment, yield reduction and erosion of pesticide efficiency. This tool allows for a multi-criteria evaluation of different fungicide applications strategies and for designing new strategies that reduce pesticide applications by increasing natural resistance linked to canopy architecture.

Weeds In Space – field-level epidemiology of herbicide resistance

David Thornby — Tue, 04 Jun 2013 15:27:49 +0300

Spatial epidemiology of herbicide resistance is insufficiently understood at present to allow us to provide quantified strategies for farmers attempting to contain or eradicate patches of resistance. SHeRA, a spatially-explicit model of herbicide-resistant weeds in patches, is a useful new tool for developing efficient strategies using a zonal management approach.

Using functional-structural plant modeling to explore the response of cotton to mepiquat chloride application and plant population density

Shenghao Gu, Jochem Evers, Lizhen Zhang, Lili Mao, Jan Vos, Zhaohu Li — Tue, 04 Jun 2013 15:29:03 +0300

The crop growth regulator Mepiquat Chloride (MC) is widely used in cotton production to optimize the canopy structure in order to maximize the yield and fiber quality. Cotton plasticity in relation to MC and other agronomical practice was quantified using a functional-structural plant model of cotton development, ultimately aiming at helping cotton farmers to manage their crops optimally.

Model assisted phenotyping of the source-sink relationships underlying the genetic diversity of sugarcane productivity

Tue, 04 Jun 2013 15:30:24 +0300

Ecomeristem, FSPM simulating sugarcane morphogenesis and plasticity depending on its nutritional status (C, H20), was used to analyze the genetic diversity of source-sink related traits controlling structural vs. non structural carbohydrate accumulation and thus sugar production. Results are discussed with respect to the challenge of FSPM assisted phenotyping and breeding.

Modelling the colonization of the decay fungus Heterobasidion annosum in Scots pine (Pinus sylvestris L.) root system

Jari Perttunen, Risto Sievänen, Tuula Piri, Tuomo Kalliokoski — Tue, 04 Jun 2013 15:31:12 +0300

We have constructed a three dimensional model that gives us structural information about the Scots pine root systems in a forest stand and the spatial distribution of roots in that stand. The model allows us to make predictions how fast Heterobasidion annosum sensu stricto colonises the pine roots, transmits from one root system to another and to recreate the distribution patterns of the pathogen in time and space.

StressMaster: a web application for dynamic modelling of the environment to assist in crop improvement for drought adaptation

Karine Chenu, Al Doherty, Greg J Rebetzke, Scott C Chapman — Tue, 04 Jun 2013 15:33:31 +0300

Drought frequently limits crop production. A modelling approach was used to characterise the water deficit that wheat plants experience over the cropping season in targeted environments. Using this insight, the StressMaster application assists in decision-making in managed environment trials to increase the probability of attaining a seasonal drought pattern that represents the targeted environments.

Arbuscular mycorrhizal fungi (AMF) diversity obtained from gooseberry plantations (Physalis peruviana) in the Colombian Andean region

María Margarita Ramírez, Fritz Oehl, Adrian Pérez, Alia Rodriguez — Tue, 04 Jun 2013 15:35:25 +0300

This research was focused on determining the relationship between arbuscular mycorrhizal fungi diversity and soil physical -chemicals properties, in gooseberry plantations in Andean Mountains from 1500 to 2700 m.o.s.l. The spore abundance, spore morphotype and diversity index were determined and analyzed through multiple regression It was possible determine that some soil conditions affect the abundance and diversity of AMF.

Adaptation of timber plantations (Gmelina arborea and Pachira quinata) with Arbuscular Mycorrhizal Fungi in the Caribbean region, Colombia

Tue, 04 Jun 2013 15:36:43 +0300

The objective was select for timber plantations, the interaction with arbuscular mycorrhizal fungi (AMF) for both, agronomic and economic aspects, in order to get forest systems well adapted to the Caribbean Region. Four AMF genera (Glomus, Acaulospora, Scutellospora and Gigaspora) and 20 ecotypes were identified from the area of study, reflecting the high diversity present in tropical forest.

CyberPlantS: a European initiative towards collaborative plant modeling

Tue, 04 Jun 2013 15:49:16 +0300

The current European research landscape of 3D plant modeling shows fragmentation and critically lacks coordination. The CyberPlantS initiative aims at creating the first European network on advanced plant simulation systems and associated e-infrastructure. The network will set up a global training strategy for innovation in computational plant modeling with a focus on plant architecture and plant-environment interactions. It is focused on the development of a new paradigm, namely cyberplants. Cyberplants refers to cybernetic systems, as biological and environmental components of vegetation exchange signals to achieve specific goals. Cyberplants also refers to cyberspace, which designates a collaborative approach based on a network community relying on a cyberinfrastructure.

Modeling parthenium weed early canopy architecture in response to environmental factors and the impacts on biological control activity of the summer rust

Ruey Toh, Kunjithapatham Dhileepan, Roger G. Shivas, Steve W. Adkins, Jim Hanan — Tue, 04 Jun 2013 15:37:34 +0300

An L-systems based 3D canopy architecture model is created for simulating and visualising the early growth of parthenium weed in response to four environmental factors (temperature, CO₂, soil moisture and plant density) and the activity of the summer rust. The outcomes provide a tool to help study the interaction between an invasive weed, a biological control agent and the environment.

Cotton fiber quality determined by fruit position, temperature and management

Xuejiao Wang, Jochem Evers, Lizhen Zhang, Lili Mao, Xuebiao Pan, Zhaohu Li — Tue, 04 Jun 2013 15:39:50 +0300

CottonXL is a tool to explore cotton fiber quality in relation to fruit position, to improve cotton quality by optimizing cotton plant structure, as well as to help farmers understand how the structure of the cotton plant determines crop growth and quality.

Mathematical Modelling of the biocontrol of Rubus alceifolius, an invasive plant in Réunion Island

Yves Dumont, Alexandre Mathieu, Serge Quilici — Tue, 04 Jun 2013 15:40:59 +0300

Invasive plants have become a major threat throughout the world, in particular in islands where the biodiversity is important and even unique. Since the 17th century, many weeds or invasive plants have been introduced in Réunion Island. Among them Rubus alceifolius, a giant bramble, is the most invasive and threatening to the endemic vegetation. After years of unsuccessful and even detrimental controls with herbicide applications and/or mechanical removal, a new biological control program has been launched, based on the release of a biocontrol agent, Cibdela janthina, a sawfly. Modelling Rubus-Cibdela interactions is not only helpfull to formalize knowledges but also to guide control strategies and decision-making, in particular before field releases. The aim of this talk, is to present a minimal mathematical model and some results based on ongoing experiments in Réunion Island.