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Eukaryotic cells maintain their inner order by a hectic process of distillation of molecular factors taking place on the surface of their lipid membranes. To understand the properties of this molecular sorting process, a physical model of…
Living organisms rely on molecular networks, such as gene circuits and signaling pathways, for information processing and robust decision-making in crowded, noisy environments. Recent advances show that interacting biomolecules…
The complexity of cellular automata is traditionally measured by their computational capacity. However, it is difficult to choose a challenging set of computational tasks suitable for the parallel nature of such systems. We study the…
Phyllotaxis, the search for the most homogeneous and dense organizations of small disks inside a large circular domain, was first developed to analyze arrangements of leaves or florets in plants. Then it has become an object of study not…
In many areas of applied geometric/numeric computational mathematics, including geo-mapping, computer vision, computer graphics, finite element analysis, medical imaging, geometric design, and solid modeling, one has to compute incidences,…
We describe an algorithm to construct an intrinsic Delaunay triangulation of a smooth closed submanifold of Euclidean space. Using results established in a companion paper on the stability of Delaunay triangulations on $\delta$-generic…
Assembly of large scale structural systems in space is understood as critical to serving applications that cannot be deployed from a single launch. Recent literature proposes the use of discrete modular structures for in-space assembly and…
Communicating cells can coordinate their gene expressions to form spatial patterns. 'Secrete-and-sense cells' secrete and sense the same molecule to do so and are ubiquitous. Here we address why and how these cells, from disordered…
In the first work of this series [physics/0204035] it was shown that the conformational space of a molecule could be described to a fair degree of accuracy by means of a central hyperplane arrangement. The hyperplanes divide the espace into…
In many tissues, cell type varies over single-cell length-scales, creating detailed spatial heterogeneities fundamental to physiological function. To gain understanding of this relationship between tissue function and detailed structure,…
In order to develop systems capable of modeling artificial life, we need to identify, which systems can produce complex behavior. We present a novel classification method applicable to any class of deterministic discrete space and time…
The hippocampus supports spatial navigation by encoding cognitive maps through collective place cell activity. We model the place cell population as non-negative spatial embeddings derived from the spectral decomposition of multi-step…
In collaborative robotic applications, human and robot have to work together during a whole shift for executing a sequence of jobs. The performance of the human robot team can be enhanced by scheduling the right tasks to the human and the…
We consider causal 3-dimensional triangulations with the topology of $S^2\times [0,1]$ or $D^2\times [0,1]$ where $S^2$ and $D^2$ are the two-dimensional sphere and disc, respectively. These triangulations consist of slices and we show that…
Meshes composed of well-centered simplices have nice orthogonal dual meshes (the dual Voronoi diagram). This is useful for certain numerical algorithms that prefer such primal-dual mesh pairs. We prove that well-centered meshes also have…
Medusa, a novel library for implementation of strong form mesh-free methods, is described. We identify and present common parts and patterns among many such methods reported in the literature, such as node positioning, stencil selection and…
This paper proposes a method for automatically monitoring and analyzing the evolution of complex geographic objects. The objects are modeled as a spatiotemporal graph, which separates filiation relations, spatial relations, and…
Spatial self-organization emerges in distributed systems exhibiting local interactions when nonlinearities and the appropriate propagation of signals are at work. These kinds of phenomena can be modeled with different frameworks, typically…
An improved neighbor list algorithm is proposed to reduce unnecessary interatomic distance calculations in molecular simulations. It combines the advantages of Verlet table and cell linked list algorithms by using cell decomposition…
The description of complex configuration is a difficult issue. We present a powerful technique for cluster identification and characterization. The scheme is designed to treat with and analyze the experimental and/or simulation data from…