An approach to multiscale modelling with graph grammars

Annals of Botany

Volumn 114, Issue 4, 2014, Pages 813-827

  Ong, Yongzhi ^a   Streit, Kataŕna ^a   Henke, Michael ^a   Kurth, Winfried ^a  

^a UNIVERSITY OF GÖTTINGEN   (Germany)

Author keywords

beech; crown growth; Fagus sylvatica; FSPM; Functional structural plant modelling; graph grammar; GroIMP; L system; metabolic network; Monte Carlo; multiscale; ozone; relational growth grammar; shikimate pathway; XL

Indexed keywords

CANOPY ARCHITECTURE; CONCEPTUAL FRAMEWORK; DATA SET; DECIDUOUS TREE; GROWTH RATE; METABOLISM; MONTE CARLO ANALYSIS; NUMERICAL MODEL; OZONE; SPATIAL ANALYSIS; TOPOLOGY; TRACE GAS;

FAGUS; FAGUS SYLVATICA;

OZONE;

ALGORITHM; ANATOMY AND HISTOLOGY; BEECH; BIOLOGICAL MODEL; COMPUTER SIMULATION; GROWTH, DEVELOPMENT AND AGING; METABOLISM; MONTE CARLO METHOD; PLANT LEAF; TREE;

ALGORITHMS; COMPUTER SIMULATION; FAGUS; METABOLIC NETWORKS AND PATHWAYS; MODELS, BIOLOGICAL; MONTE CARLO METHOD; OZONE; PLANT LEAVES; TREES;

EID: 84910613555     PISSN: 03057364     EISSN: 10958290     Source Type: Journal    
DOI: 10.1093/aob/mcu155     Document Type: Article

References (53)

1. Band LR, Fozard JA, Godin C, et al. 2012. Multiscale systems analysis of root growth and development: modeling beyond the network and cellular scales. The Plant Cell 24: 3892-3906
2. Betz GA, Knappe C, Lapierre C, et al. 2009. Ozone affects shikimate pathway transcripts and monomeric lignin composition in European beech (Fagus sylvatica L). European Journal of Forest Research 128: 109-116
3. Bird RB, Armstrong RC, Hassager O. 1987. Dynamics of polymeric liquids, 2nd edn. New York: JohnWiley
4. Boudon F, Prusinkiewicz P, Federl P, Godin C, Karwowski R. 2003. Interactive design of bonsai tree models. Computer Graphics Forum 22: 591-599
5. Boudon F, Pradal C, Cokelaer T, Prusinkiewicz P, Godin C. 2012. L-Py: an L-System simulation framework for modeling plant development based on a dynamic language. Frontiers in Plant Science 3: 76
6. Brandt A. 2002. Multiscale scientific computation: review 2001. In: Barth TJ, Chan T, Haimes R, eds. Multiscale and multiresolution methods: theory and applications. Berlin: Springer, 3-96
7. Buck-Sorlin G, Kniemeyer O, Kurth W. 2005. Barley morphology, genetics and hormonal regulation of internode elongation modelled by a relational growth grammar. New Phytologist 166: 859-867
8. Car R, Parrinello M. 1985. Unified approach for molecular dynamics and density-functional theory. Physical Review Letters 55: 2471-2474
9. Chiba N, Ohkawa S, Muraoka K, Miura M. 1994. Visual simulation of botanical trees based on virtual heliotropism and dormancy break. Journal of Visualization and Computer Animation 5: 3-15
10. Cochard H, Tyree MT. 1990. Xylem dysfunction in Quercus: vessel sizes, tyloses, cavitation and seasonal changes in embolism. Tree Physiology 6: 393-407
11. Cochard H, Coste S, Chanson B, Guehl J, Nicolini E. 2005. Hydraulic architecture correlates with bud organogenesis and primary shoot growth in beech (Fagus sylvatica). Tree Physiology 25: 1545-1552
12. Cournède P-H, Mathieu A, Houllier F, Barthélémy D, de Reffye P. 2008. Computing competition for light in the GREENLAB model of plant growth: a contribution to the study of the effects of density on resource acquisition and architectural development. Annals of Botany 101: 1207-1219
13. DaSilva D, Boudon F, Godin C, Hervé S. 2008. Multiscale framework for modeling and analyzing light interception by trees. Multiscale Modeling and Simulation 7: 910-933
14. Dada JO, Mendes P. 2011. Multi-scale modelling and simulation in systems biology. Integrative Biology 3: 86-96
15. Denby B, Sundvor I, Cassiani M, de Smet P, de Leeuw F, Hoŕalek J. 2010. Spatial mapping of ozone and SO2 trends in Europe. Science of the Total Environment 408: 4795-4806
16. Deussen O, Hanrahan P, Lintermann B, Měch R, Pharr M, Prusinkiewicz P. 1998. Realistic modeling and rendering of plant ecosystems. In: Cunningham S, Bransford W, Cohen MF, eds. SIGGRAPH 98 Proceedings of the 25st Annual Conference on Computer Graphics and Interactive Techniques, Orlando, Florida. New York: ACM Press, 275-286
17. E W. 2011. Principles of multiscale modeling. Cambridge: Cambridge University Press
18. E W, Engquist B. 2003. The heterogeneous multiscale methods. Communications in Mathematical Sciences 1: 87-132
19. Ganter B. 2005.Contextual attribute logic of many-valued attributes. In: Ganter B, Stumme G, Wille R, eds. Formal concept analysis: foundations and applications. Berlin: Springer, 101-113
20. Godin C, Caraglio Y. 1998. A multiscale model of plant topological structures. Journal of Theoretical Biology 191: 1-46
21. Han L, Gresshoff PM, Hanan J. 2010. A functional-structural modelling approach to autoregulation of nodulation. Annals of Botany 107: 855-863
22. Hanan J. 1992. Parametric L-systems and their application to the modelling and visualization of plants. PhD Thesis, University of Regina, Canada
23. Hanan J. 2013. Functional-structural modelling with L-systems: where from and where to. In: Sievänen R, Nikinmaa E, Godin C, Lintunen A, Nygren P, eds. Proceedings of the 7th International Conference on Functional-Structural Plant Models, Saariselkä , Finland, June 2013. Finland: Finnish Society of Forest Science, Finnish Forest Research Institute, Department of Forest Sciences, University of Helsinki, 1-3
24. Harper JL, Rosen BR, White J. 1986. The growth and form of modular organisms. London: The Royal Society
25. Hemmerling R, Kniemeyer O, Lanwert D, Kurth W, Buck-Sorlin G. 2008. The rule-based language XL and the modelling environment GroIMP illustrated with simulated tree competition. Functional Plant Biology 35: 739-750
26. Ho QT, Verboven P, Verlinden BE, et al. 2011.Athree-dimensional multiscale model for gas exchange in fruit. Plant Physiology 155: 1158-1168
27. Kalos MH, Whitlock PA. 2008. Monte Carlo methods, 2nd edn. Weinheim: Wiley-VCH
28. Kang M-Z, de Reffye P. 2007. A mathematical approach estimating source and sink functioning of competing organs. In: Vos J, Marcelis LFM, de Visser PHB, Struik PC, Evers JB, eds. Functional-structural plant modelling in crop production. Berlin: Springer, 65-74
29. Kerner R, Winkler J, Dupuy J, et al. 2011. Changes in the proteome of juvenile European beech following three years exposure to free-Air elevated ozone. iForest 4: 69-76
30. Kevrekidis IG, Gear CW, Hyman JM, Kevrekidis PG, Runborg O, Theodoropoulos C. 2003. Equation-free, coarse-grained multiscale computation: enabling microscopic simulators to perform system-level analysis. Communications in Mathematical Sciences 1: 715-762
31. Kleijnen JPC. 1992. Sensitivity analysis of simulation experiments: regression analysis and statistical design. Mathematics and Computers in Simulation 34: 297-315
32. Knauer U. 2011. Algebraic graph theory: morphisms, monoids and matrices. Berlin: Walter De Gruyter
33. Kniemeyer O. 2008. Design and implementation of a graph grammar based language for functional-structural plant modelling. PhD Thesis, University of Technology at Cottbus, Germany
34. Kniemeyer O, Buck-Sorlin G, Kurth W. 2007. GroIMP as a platform for functional-structural modelling of plants. In: Vos J, Marcelis LFM, de Visser PHB, Struik PC, Evers JB, eds. Functional-structural plant modelling in crop production. Dordrecht: Springer, 43-52
35. Kurth W, Kniemeyer O, Buck-Sorlin G. 2005.Relational growth grammars-A graph rewriting approach to dynamical systems with a dynamical structure. In: Banâtre J-P, Fradet P, Giavitto J-L, Michel O, eds. Unconventional programming paradigms. Lecture Notes in Computer Science 3566. Berlin: Springer, 56-72
36. Lane B, Prusinkiewicz P. 2002. Generating spatial distributions for multilevel models of plant communities. In: McCool MD. ed. Proceedings of Graphics Interface 2002, Calgary, Alberta, May 2002. Canadian Human-Computer Communications Society, 69-80
37. Lemoine D, Cochard H, Granier A. 2002.Within crown variation in hydraulic architecture in beech (Fagus sylvatica L): evidence for a stomatal control of xylem embolism. Annals of Forest Science 59: 19-27
38. Lindenmayer A. 1968.Mathematical models for cellular interaction in development. Journal of Theoretical Biology 18: 280-315
39. Lintunen A, Sievänen R, Kaitaniemi P, Perttunen J. 2011. Models of 3D crown structure for Scots pine (Pinus sylvestris) and silver birch (Betula pendula) grown in mixed forest. Canadian Journal of Forest Research 41: 1779-1794
40. Lohr SL. 2009. Sampling: design and analysis, 2nd edn. Boston: Cengage Learning
41. Olbrich M, Gerstner E, Bahnweg G, et al. 2010. Transcriptional signatures in leaves of adult European beech trees (Fagus sylvatica L) in an experimentally enhanced free air ozone setting. Environmental Pollution 158: 977-982
42. Ong Y, Kurth W. 2012. A graph model and grammar for multi-scale modelling using XL. In: Gao J, DubitzkyW, WuC, et al., eds. 2012 IEEE International Conference on Bioinformatics and Biomedicine Workshops, Philadelphia, USA, October 2012. USA: IEEE Computer Society, 1-8
43. Palubicki W, Horel K, Longay S, et al. 2009. Self-organizing tree models for image synthesis. ACM Transactions on Graphics 28(3): 58: 1-58: 10
44. Prusinkiewicz P, Hammel M, Hanan J, Měch R. 1997. Visual models of plant development. In: Rozenberg G, Salomaa A, eds. Handbook of formal languages. Heidelberg: Springer, 535-597
45. Prusinkiewicz P, Muendermann L, Karwowski R, Lane R. 2001. The use of positional information in the modeling of plants. In: Fiume E, ed. SIGGRAPH 01 Proceedings of the 28th Annual Conference on Computer Graphics And Interactive Techniques, Los Angeles, California. New York: ACM Press, 289-300
46. Scalfi M, Troggio M, Piovani P, et al. 2004. A RAPD, AFLP and SSR linkage map, and QTL analysis in European beech (Fagus sylvatica L). Theoretical and Applied Genetics 108: 433-441
47. Schober R. 1995. Ertragstafeln wichtiger Baumarten. Frankfurt am Main: J. D. Sauerländer's Verlag
48. Schön M. 2014. Structural-functional concepts in forest modeling applicable for higher resolution of forest ecosystem simulations. PhD Thesis, Technical University in Zvolen, Slovak Republic
49. Seidl R, Rammer W, Scheller RM, Spies TA. 2012. An individual-based process model to simulate landscape-scale forest ecosystem dynamics. Ecological Modelling 231: 87-100
50. Sievänen R, Nikinmaa E, Godin C, Lintunen A, Nygren P. 2013. Proceedings of the 7th International Conference on Functional-Structural Plant Models. Finland: Finnish Society of Forest Science, Finnish Forest Research Institute, Department of Forest Sciences, University of Helsinki
51. Strobel J. 2004. Die Atmung der verholzten Organe von Altbuchen (Fagus sylvatica L) in einem Kalk-und einem Sauerhumusbuchenwald. PhD Thesis, University of Göttingen, Germany
52. Warshel A, Levitt M. 1976. Theoretical studies of enzymic reactions: dielectric, electrostatic and steric stabilization of the carbonium ion in the reaction of lysozyme. Journal of Molecular Biology 103: 227-249
53. WuQ-L, Cournède P-H, Mathieu A. 2012. An efficient computational method for global sensitivity analysis and its application to tree growth modelling. Reliability Engineering and System Safety 107: 35-43