Tessellations and Pattern Formation in Plant Growth and Development

The shoot apical meristem (SAM) is a dome-shaped collection of cells at the apex of growing plants from which all above-ground tissue ultimately derives. In Arabidopsis thaliana (thale cress), a small flowering weed of the Brassicaceae family (related to mustard and cabbage), the SAM typically contains some three to five hundred cells that range from five to ten microns in diameter. These cells are organized into several distinct zones that maintain their topological and functional relationships throughout the life of the plant. As the plant grows, organs (primordia) form on its surface flanks in a phyllotactic pattern that develop into new shoots, leaves, and flowers. Cross-sections through the meristem reveal a pattern of polygonal tessellation that is suggestive of Voronoi diagrams derived from the centroids of cellular nuclei. In this chapter we explore some of the properties of these patterns within the meristem and explore the applicability of simple, standard mathematical models of their geometry.Comment: Originally presented at: "The World is a Jigsaw: Tessellations in the Sciences," Lorentz Center, Leiden, The Netherlands, March 200

SBML Level 3: an extensible format for the exchange and reuse of biological models

Systems biology has experienced dramatic growth in the number, size, and complexity of computational models. To reproduce simulation results and reuse models, researchers must exchange unambiguous model descriptions. We review the latest edition of the Systems Biology Markup Language (SBML), a format designed for this purpose. A community of modelers and software authors developed SBML Level 3 over the past decade. Its modular form consists of a core suited to representing reaction-based models and packages that extend the core with features suited to other model types including constraint-based models, reaction-diffusion models, logical network models, and rule-based models. The format leverages two decades of SBML and a rich software ecosystem that transformed how systems biologists build and interact with models. More recently, the rise of multiscale models of whole cells and organs, and new data sources such as single-cell measurements and live imaging, has precipitated new ways of integrating data with models. We provide our perspectives on the challenges presented by these developments and how SBML Level 3 provides the foundation needed to support this evolution

Fast and Globally Convergent Pose Estimation From Video Images

Determining the rigid transformation relating 2D images to known 3D geometry is a classical problem in photogrammetry and computer vision. Heretofore, the best methods for solving the problem have relied on iterative optimization methods which cannot be proven to converge and/or which do not effectively account for the orthonormal structure of rotation matrices. We show that the pose estimation problem can be formulated as that of minimizing an error metric based on collinearity in object (as opposed to image) space. Using object space collinearity error, we derive an iterative algorithm which directly computes orthogonal rotation matrices and which is globally convergent. Experimentally, we show that the method is computationally efficient, that it is no less accurate than the best currently employed optimization methods, and that it outperforms all tested methods in robustness to outliers. Chien-Ping Lu, Silicon Graphics Inc. [email protected] y Greg Hager, Department of Computer..

Fast and globally convergent pose estimation from video images

AbstractÐDetermining the rigid transformation relating 2D images to known 3D geometry is a classical problem in photogrammetry and computer vision. Heretofore, the best methods for solving the problem have relied on iterative optimization methods which cannot be proven to converge and/or which do not effectively account for the orthonormal structure of rotation matrices. We show that the pose estimation problem can be formulated as that of minimizing an error metric based on collinearity in object (as opposed to image) space. Using object space collinearity error, we derive an iterative algorithm which directly computes orthogonal rotation matrices and which is globally convergent. Experimentally, we show that the method is computationally efficient, that it is no less accurate than the best currently employed optimization methods, and that it outperforms all tested methods in robustness to outliers. Index TermsÐPose estimation, absolute orientation, optimization,weak-perspective camera models, numerical optimization.

APPLICATION OF A GENERALIZED MWC MODEL FOR THE MATHEMATICAL SIMULATION OF METABOLIC PATHWAYS REGULATED BY ALLOSTERIC ENZYMES

In our effort to elucidate the systems biology of the model organism, Escherichia coli, we have developed a mathematical model that simulates the allosteric regulation for threonine biosynthesis pathway starting from aspartate. To achieve this goal, we used kMech, a Cellerator language extension that describes enzyme mechanisms for the mathematical modeling of metabolic pathways. These mechanisms are converted by Cellerator into ordinary differential equations (ODEs) solvable by Mathematica *These authors contributed equally to this work Biology correspondence should be addressed to G.W.H