Integration of the xylem sap flow model HYDRA and of a soil water model into a rule-based framework and test at oak and spruce trees

PhD topic D4

Integration of the xylem sap flow model HYDRA and of a soil water model into a rule-based framework and test at oak and spruce trees

Description:

The model HYDRA was designed 15 years ago as a simulator for water potential and flux in the xylem in branched tree crowns. It was based on physical laws and implemented in the language C (Früh 1995, 1997). Structural information about the tree crowns was taken from L-system-based morphological tree models and fed into HYDRA by a dedicated interface from the software GROGRA (Kurth 1994), taking numerical requirements for the resolution of the spatial discretization into account. This allowed to produce spatial and temporal profiles of water potential and flow along selected pathways in trees and to compare the hydraulic architecture of different coniferous species (Kurth & Früh 1999). Later on, the model was extended to include microclimatic effects and stomatal conductance regulation, and it was adapted and applied to young deciduous trees (oak; Kurth & Schulte 2003, Sloboda & Leuschner 2003). Furthermore, interfaces to external microclimatic and soil-hydraulic simulation models, running on other platforms, were technically realized (Anzola Jürgenson 2002, Dzierzon et al. 2007), but were never thoroughly used and validated due to their heterogeneity and complexity. The comparison of HYDRA model runs with sap flow measurements at young oak trees showed huge discrepancies which are not yet completely resolved (Sloboda & Leuschner 2003).

Meanwhile, a new generation of tools for functional-structural plant modelling became available, particularly the graph-grammar based simulation platform GroIMP, which was used for modelling growth and architecture of various tree species and which contains already a simulator for radiation distribution and light interception. Recently, methods for efficient and stable solution of ordinary differential equations were included (Hemmerling et al. 2010). This progress should now make it possible to get rid of the necessity to combine several different software systems which are not tuned to communicate with each other, and instead to realize a coherent simulator on the platform GroIMP for the whole system soil - plant - atmosphere, including soil water dynamics, plant growth and hydraulics, and microclimatic drivers for transpiration and stomatal regulation. By the greater transparency of the rule-based language XL (an extension of Java), which is supported by GroIMP, and by the improved consistency of submodels which then will all be realized in the same formal framework, the analysis of the behaviour of the model and its validation and possible modification will become tractable. Data from earlier measurements and model runs will be used. Collaboration with teams specialized in hydraulic measurements and simulation will be encouraged; earlier contacts of the department to such teams will be resumed.

Literature:

Anzola Jürgenson, G. A. (2002): Linking structural and process-oriented models of plant growth. Development and test of the software NEXUS as a multiple interface for functional-structural models. Ph.D. thesis, Fakultät für Forstwissenschaften und Waldökologie, University of Göttingen (185 pp.). http://webdoc.sub.gwdg.de/diss/2003/anzola/anzola.pdf
Dzierzon, H.; Schulte, M.; Blendinger, Ch.; Sloboda, B.; Kurth, W. (2007): Enhancing the simulation of a hydraulic tree-soil system by an interface between the hydraulic models HYDRA for Quercus petraea (Matt.) Liebl. and the hydraulic soil model SilVlow. Poster on the "5th International Workshop on Functional-Structural Plant Modelling" (FSPM07), Napier (New Zealand), 4.-9. 11. 2007. http://www.uni-forst.gwdg.de/~wkurth/dzierzon_napier.pdf
Früh, Th. (1997): Simulation of water flow in the branched tree architecture. Silva Fennica, 31 (1997), 275-284. https://helda.helsinki.fi/bitstream/handle/1975/8526/silva_1997_31_3_(4)_fruh.t.pdf?sequence=3
Früh, Th. (1995): Entwicklung eines Simulationsmodells zur Untersuchung des Wasserflusses in der verzweigten Baumarchitektur. Berichte des Forschungszentrums Waldökosysteme, Universität Göttingen, Ser. A, 131 (192 pp.).
Früh, Th.; Kurth, W. (1999): The hydraulic system of trees: Theoretical framework and numerical simulation. J. Theor. Biol., 201, 251-270. http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.37.754&rep=rep1&type=pdf
GroIMP: http://www.grogra.de
Hemmerling, R.; Smolenová, K.; Kurth, W. (2010): A programming language tailored to the specification and solution of differential equations describing processes on networks. In: Adrian-Horia Dediu, Henning Fernau, Carlos Martín-Vide (eds.), Language and Automata Theory and Applications. 4th International Conference, LATA 2010, Trier, May 24-28, 2010, Lecture Notes in Computer Science 6031, Springer, Berlin etc., 297-308.
Kniemeyer, O. (2008): Design and Implementation of a Graph Grammar Based Language for Functional-Structural Plant Modelling. Ph.D. thesis, University of Technology at Cottbus. [http://nbn-resolving.de/urn/resolver.pl?urn=urn:nbn:de:kobv:co1-opus-5937]
Kurth, W. (1994): Growth Grammar Interpreter GROGRA 2.4: A software tool for the 3-dimensional interpretation of stochastic, sensitive growth grammars in the context of plant modelling. Introduction and Reference Manual. 190 p. Berichte des Forschungszentrums Waldökosysteme, Universität Göttingen, Ser. B, Vol. 38. http://www.uni-forst.gwdg.de/~wkurth/cb/html/gro.ps.gz
Kurth, W.; Schulte, M. (2003): Numerical simulation of the hydraulic system of trees: The case of Durmast Oak (Quercus petraea [Matt.] Liebl.). http://www.uni-forst.gwdg.de/~wkurth/pro_tf.html
Sloboda, B.; Leuschner, Ch. (2003): Numerische Simulation des hydraulischen Systems Baum - Boden bei der Traubeneiche (Quercus petraea [Matt.] Liebl.). Project report (58 pp.) http://www.uni-forst.gwdg.de/~wkurth/ber_l_schulte.pdf