Browsing by Author "Prusinkiewicz, Przemyslaw"
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Item Open Access A biomechanical model of branch shape in plants expressed using L-systems(2000) Jirasek, Catherine Alena; Prusinkiewicz, PrzemyslawItem Open Access A Computational Study of Tree Architecture(2013-01-18) Palubicki, Wojtek; Prusinkiewicz, PrzemyslawSince their inception in the 1970s, architectural tree models (Hallé et al. 1978) have provided the dominant framework for describing tree forms. An architectural tree model is viewed as a “genetic blueprint” of tree development: a precise developmental pattern subject to disruptive modifications by the environment (Hallé et al. 1978, p. 74): Organization in plants reflects the precisely controlled genetic program, which determines their development. [...] This program is disrupted by exogenous, environmental factors.” On the basis of extensive field data, Halle, Oldeman and Tomlinson distinguished 23 such programs and postulated that they capture the diversity of trees observed in nature. An alternative perspective of tree form was proposed by Sachs and Novoplansky (1995). They viewed environmentally-mediated interactions – in particular, competition between buds and branches for light and space – not merely as a modifier, but as a key determinant of tree form. According to their perspective, genetic and molecular mechanisms do not define tree forms directly, but only set up the rules for tree self-organization through competition between branches (Sachs and Novoplansky 1995): “The form of a tree is generated by self-organization in which alternative branches compete with one another, following no strict plan or pre-pattern.” In spite of the apparent dichotomy between both views, Sachs and Novoplansky postulated that architectural models and self-organization have a complementary character and the diversity of tree forms in nature results from an interplay between them. Here in this thesis I examine the concepts of architectural models, self-organization, and their synthesis in light of computer models implementing these paradigms. In particular, among the results is presented a theoretical morphospace constructed by only a small number of model parameters that captures major characteristics of most of the architectural models. Hallé, F., Oldeman, R. A., & Tomlinson, P. B. (1978). Tropical trees and forests. Berlin: Springer-Verlag. Sachs, T., & Novoplansky, A. (1995). Tree from: Architectural models do not suffice. Israel Journal of Plant Sciences 43, 203–212.Item Open Access A physically-based model of folded surfaces with application to plant leaves(1997) Dimian, Daniel M.; Prusinkiewicz, PrzemyslawItem Open Access An Exploration of the Emergence of Pattern and Form from Constraints on Growth(2014-09-15) Dale, Holly; Prusinkiewicz, Przemyslaw; Hobill, DavidGrowing structures are subjects of the space in which they develop. When space is limited or growth is constrained complex patterns and formations can arise. One example of this is seen in the bark patterns of trees. The rigid outer bark layer constrains the growth of the inner layers, resulting in the formation of intricate fracture patterns. An understanding of bark pattern formation has been hampered by insufficient information regarding the biomechanical properties of bark and the corresponding difficulties in faithfully modeling bark fractures using continuum mechanics. Grasstrees, however, have a discrete bark-like structure, making them particularly well suited for computational studies. In this thesis I present a model of grasstree development capturing both primary and secondary growth. A biomechanical model based on a mass-spring network represents the surface of the trunk, permitting the emergence of fractures. This model reproduces key features of grasstree bark patterns which have the same statistical character as trees found in nature. The results support the general hypothesis that the observed bark patterns found in grasstrees may be explained in terms of mechanical fractures driven by secondary growth and that bark pattern formation is primarily a biomechanical phenomenon. Furthermore, I extend the grasstree model to analyze the patterning of discrete elements on the surface of pandanus fruit. Pandanus fruit also exhibit patterns apparently related to fracturing and constraints of space. In this case, the results show that the pattern is likely a result of a higher level mechanisms as opposed to purely biomechanical.Item Open Access Annotation of Vascular Plant Structures using Haptic Assistance(2022-08-16) Gu, Philmo; Prusinkiewicz, Przemyslaw; Jacob, Christian; Alim, UsmanThe vascular structure within a plant is a network of vascular bundles that transport nutrients and water. Analyzing the organization of vascular bundles can lead to a better understanding of the vascular structure's role in the development of plants. One way to analyze the vascular structure is by scanning plant samples using X-ray micro-CT and then annotate the volumetric data digitally. However, this process is challenging due to the complex arrangement of vascular bundles and lack of contrast from other nearby anatomic structures. To address these problems, we developed a system to annotate the vascular structure of plant samples using force feedback to interact with the surface of objects and along the centerline of tubular structures. This system annotated the vascular structure of flower heads such as Gerbera hybrida, and inflorescences such as Arabidopsis thaliana. User study participants found the haptic assistance helpful for interacting with and annotating plant samples.Item Open Access Application of implicit methods to the interactive modeling of trees(2010) Kochhar, Vishal; Prusinkiewicz, Przemyslaw; Wyvill, BrianItem Open Access Artificial evolution of generative models in computer graphics(1993) MacKenzie, Cameron; Prusinkiewicz, PrzemyslawItem Open Access Biomechanics in botanical trees(2005) Taylor-Hell, Julia; Prusinkiewicz, PrzemyslawItem Open Access Cell Complexes: The Structure of Space and the Mathematics of Modularity(2015-09-29) Lane, Brendan Joseph; Prusinkiewicz, PrzemyslawThe modeling of growing multicellular structures is of fundamental importance in investigating plant development. A distinctive feature of plants is that, with rare exceptions, cells do not move with respect to each other; the only differences in tissue topology are due to cell divisions. Corresponding features are found in other application domains, such as geometric modeling. Models from these diverse domains, taken together, constitute the field of developmental modeling. This dissertation is concerned with devising a mathematical and computational formalism for such modeling. Examining simple examples of one-dimensional models shows that the mathematical structure of the cell complex is ideal for developmental modeling. The cell complex consists of mathematical cells of different dimensions, letting physical quantities of different inherent dimension sit in their proper place in the structure. A cell complex can be represented in an index-free manner, and topological operations on it, including the important case of cell division, can be effected in a local manner. Finally, the cell complex is built on neighbourhood relations which let developmental rules easily access values in neighbouring cells. A novel data structure, the flip, records a single adjacency between cells in a cell complex; a flip table, the collection of all flips in the complex, is in turn sufficient to represent the complex itself. This representation is used to build the Cell Complex Framework, a C++ API which can be used for computational modeling of development in any number of dimensions. The framework provides basic operations such as iterating over a cell complex, adding, removing, dividing, and merging cells, and computing geometric information such as orientation, measure, and centroid. Some developmental models from the existing literature, in both two and three dimensions, are reproduced using the Cell Complex Framework, demonstrating its workability and expressiveness; these include both geometric models as well as models of biological systems. New models are also shown, including a model of turtle geometry on the surface of a 2D mesh and a three-dimensional model of the apex of the moss Physcomitrella patens.Item Open Access Computational Modeling of Leaf Development and Form(2014-12-24) Runions, Adam; Prusinkiewicz, PrzemyslawLeaves are a functionally important and visually conspicuous aspect of plant form. In nature, they present with a great diversity of shapes ranging, for example, from simple poplar leaves to prominently lobed maples through to highly compound tomato leaves. In this thesis, I examine the basis of this diversity using computer simulations. To elucidate the biological determinants of leaf form I first present three case studies focused on different aspects of leaf development. The first simulates leaf and midvein initiation in Brachypodium distachyon, and reproduces detailed biological observations of these processes. The remaining focus on leaf margin development, which is thought to play a primary morphogenetic role in the acquisition of leaf form. Thus for the second and third case studies, I propose a model of leaf margin development for simple leaves in Arabidopsis thaliana and compound leaves in Cardamine hirsuta. To simulate leaf margin development the boundary propagation method is proposed, which simulates the leaf margin and its propagation during development. The models developed using this method are qualitatively consistent with biological observations, and elucidate the role of the margin during simple and compound leaf development. To investigate natural leaf form diversity I propose a geometric model of leaf development based on the three molecularly detailed case-studies. This framework simulates leaf development as an interplay between patterning of the leaf margin, the establishment and growth of veins and the progression of maturation in the leaf blade. Although couched in geometric terms, the method is derived from the molecular level models developed in the three case studies, and is thus biologically motivated. This facilitates a biologically meaningful exploration of the diversity of leaf forms seen in nature using the framework. Additionally, it provides a procedural technique for generating leaf forms for computer graphics purposes.Item Open Access Design and implementation of global virtual laboratory: a network accessible simulation environment(1997) Federl, Pavol; Prusinkiewicz, PrzemyslawItem Open Access Differential L-systems and their application to the simulation and visualisation of plant development(1996) Hammel, Mark Stephen; Prusinkiewicz, PrzemyslawItem Open Access Evolutionary design of 2D fractals and 3D plant structures for computer graphics(2004) Yu, Jing; Jacob, Christian; Prusinkiewicz, PrzemyslawItem Open Access Extensions to the virtual laboratory(1995) Lowe, Earle Morven; Prusinkiewicz, PrzemyslawItem Open Access Genetic interactions in the development of spatial patterns in bacteria(2007) Davidson, Carla Jean; Surette, Michael; Prusinkiewicz, PrzemyslawItem Open Access Graphical modeling using L-systems and particle systems: a comparison(1993) Orth, Thomas; Prusinkiewicz, PrzemyslawItem Open Access Hairs, Textures, and Shades: Improving the Realism of Plant Models Generated with L-Systems(2005-08) Fuhrer, Martin; Prusinkiewicz, Przemyslaw; Wyvill, Brian; Costa Sousa, Mário; Hushlak, GeraldItem Open Access Hybrid sketch-based and procedural modeling of plants(2007) Anastacio, Fabricio Cesar Ferreira; Costa Sousa, Mário; Prusinkiewicz, PrzemyslawItem Open Access Improving the process of plant modeling: the L+C modeling language(2002) Karwowski, Radoslaw Mateusz; Prusinkiewicz, PrzemyslawItem Open Access Interactive Evolutionary Modelling by Duplication and Diversification of L-Systems(2013-07-15) Burt, Thomas; Prusinkiewicz, PrzemyslawEvolutionary processes are responsible for the wide variety of organic forms seen in the natural world. Digital simulations inspired by these processes can be used to create diverse models for computer imagery purposes. In the case of interactive evolutionary computation (IEC), a modeler affects the resulting forms by guiding evolutionary processes. This guidance can be achieved using very simple interfaces, thus putting IEC in the hands of a broad class of users. In our work we focus on the application of IEC to plant modeling. The individual plants are generated using L-systems. Evolution of L-systems is particularly appealing due to analo- gies that can be drawn between genetic code and L-system productions. Several attempts to evolve L-system-based models have been devised in the past by different authors using the standard operations of genetic algorithms — mutations and crossover — to modify the productions. We have improved on these results by considering a different set of operations — duplication and diversification — as the basis of L-system evolution instead. These oper- ations reflect the widely accepted theory of evolution of genetic material, according to which gene duplication is the first step in smooth transitions from less complex to more complex phenotypes via gradual diversification of redundant genetic material. This thesis investi- ages how this general principle can be adapted to the evolution of L-systems, presents an interactive modeling system based on the resulting theory, and illustrates the results using numerous visual examples.
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