title: Framework for efficient synthesis of spatially embedded morphologies.
abstract: Many problems in science and engineering require the ability to grow tubular or polymeric structures up to large volume fractions within a bounded region of three-dimensional space. Examples range from the construction of fibrous materials and biological cells such as neurons, to the creation of initial configurations for molecular simulations. A common feature of these problems is the need for the growing structures to wind throughout space without intersecting. At any time, the growth of a morphology depends on the current state of all the others, as well as the environment it is growing in, which makes the problem computationally intensive. Neuron synthesis has the additional constraint that the morphologies should reliably resemble biological cells, which possess nonlocal structural correlations, exhibit high packing fractions, and whose growth responds to anatomical boundaries in the synthesis volume. We present a spatial framework for simultaneous growth of an arbitrary number of nonintersecting morphologies that presents the growing structures with information on anisotropic and inhomogeneous properties of the space. The framework is computationally efficient because intersection detection is linear in the mass of growing elements up to high volume fractions and versatile because it provides functionality for environmental growth cues to be accessed by the growing morphologies. We demonstrate the framework by growing morphologies of various complexity.
authors.affiliation: Blue Brain Project, École Polytechnique Fédérale de Lausanne, Geneva, Switzerland.
authors.forename: Liesbeth
authors.initials: L
authors.lastname: Vanherpe
authors.affiliation: Blue Brain Project, École Polytechnique Fédérale de Lausanne, Geneva, Switzerland.
authors.forename: Lida
authors.initials: L
authors.lastname: Kanari
authors.affiliation: Blue Brain Project, École Polytechnique Fédérale de Lausanne, Geneva, Switzerland.
authors.forename: Guy
authors.initials: G
authors.lastname: Atenekeng
authors.affiliation: Blue Brain Project, École Polytechnique Fédérale de Lausanne, Geneva, Switzerland.
authors.forename: Juan
authors.initials: J
authors.lastname: Palacios
authors.affiliation: Blue Brain Project, École Polytechnique Fédérale de Lausanne, Geneva, Switzerland.
authors.forename: Julian
authors.initials: J
authors.lastname: Shillcock