- Graph theory, formal grammars, functional-structural plant models, simulation, upscaling, fluid modeling/CFD

Model of the branch of an apple tree with fruits: water- and sugar-flows in xylem and phloem, water- and sugar-loading of the fruits, leaf transpiration, collection of radiation and carbon dioxide by the leaves, model of photosynthesis (G. Buck-Sorlin).

Distribution of negative water-pressure in model-plant (simulation)
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- Johannes Merklein, M. Poirier-Pocovi, G. Buck-Sorlin, W. Kurth, Q. Long (2018): A dynamic model of xylem and phloem flux in an apple branch. IEEE Proceedings of the 6th IEEE International Symposium on Plant Growth Modeling, Simulation, Visualization and Applications, Nov 4-8, 2018 Hefei/China (accepted).
- Johannes Merklein (2014): Modellierung turbulenter Strömungen mit Anwendungsfällen in der Bioklimatologie und Astrophysik. (Dissertation)
- Johannes Merklein, Jelka Braden, Claus Döring, Oleg Panferov (2013): Ermittlung des künftigen Sturmrisikos für Waldökosysteme im Solling, Niedersachsen. (Calculations of turbulence and wind fields in 3D-landscape with vegetation. Talk at KLIFF-conference in September 2013 in Göttingen)
- Iapichino, L.; Schmidt, W.; Niemeyer, J.C.; Merklein, J. (2011): Turbulence production and turbulent pressure support in the intergalactic medium, MNRAS (Monthly Notices of the Royal Astronomical Society),05.04.2011, DOI: 10.1111/j.1365-2966.2011.18550.x
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