Related papers: Minimal branching and fusion morphogenesis approac…
Large-scale structural patterns commonly occur in network models of complex systems including a skewed node degree distribution and small-world topology. These patterns suggest common organizational constraints and similar functional…
In biological systems, the growth of cells, tissues, and organs is influenced by mechanical cues. Locally, cell growth leads to a mechanically heterogeneous environment as cells pull and push their neighbors in a cell network. Despite this…
Morphogenesis emerges from dynamic feedback among geometry, mechanics, and chemistry; however, disentangling these contributions in living systems remains challenging. Here, we focus on the interplay between geometry and mechanics by…
Interactions between neighboring cells are essential for generating or refining patterns in a number of biological systems. We propose a discrete filtering approach to predict how networks of cells modulate spatially varying input signals…
We discuss shape profiles emerging in inhomogeneous growth of squeezed tissues. Two approaches are used simultaneously: i) conformal embedding of two-dimensional domain with hyperbolic metrics into the plane, and ii) a pure energetic…
Modular structure is ubiquitous among complex networks. We note that most such systems are subject to multiple structural and functional constraints, e.g., minimizing the average path length and the total number of links, while maximizing…
Both natural and engineered supply networks exhibit universal structural patterns, such as the formation of loops, yet the principles governing optimal structures remain unclear. These patterns can be interpreted as solutions of…
Neural connectivity at the cellular and mesoscopic level appears very specific and is presumed to arise from highly specific developmental mechanisms. However, there are general shared features of connectivity in systems as different as the…
A long-standing challenge is designing multi-scale structures with good connectivity between cells while optimizing each cell to reach close to the theoretical performance limit. We propose a new method for direct multi-scale topology…
Characterization of the differences between biological and random networks can reveal the design principles that enable the robust realization of crucial biological functions including the establishment of different cell types. Previous…
We introduce a model of traveling agents ({\it e.g.} frugivorous animals) who feed on randomly located vegetation patches and disperse their seeds, thus modifying the spatial distribution of resources in the long term. It is assumed that…
The mathematical framework of multiplex networks has been increasingly realized as a more suitable framework for modelling real-world complex systems. In this work, we investigate the optimization of synchronizability in multiplex networks…
This work presents a framework for modeling three-dimensional scaffold-mediated bone regeneration and the associated optimization problem. By incorporating microstructure into the model through periodic homogenization, we capture the…
We investigate hybrid linear-morphological networks. Recent studies highlight the inherent affinity of morphological layers to pruning, but also their difficulty in training. We propose a hybrid network structure, wherein morphological…
Let a collection of networks represent interactions within several (social or ecological) systems. We pursue two objectives: identifying similarities in the topological structures that are held in common between the networks and clustering…
Distribution networks -- from vasculature to urban transportation systems -- are prevalent in both the natural and consumer worlds. These systems are intrinsically physical in composition and are embedded into real space, properties that…
Many-to-one maps are ubiquitous in machine learning, from the image recognition model that assigns a multitude of distinct images to the concept of "cat" to the time series forecasting model which assigns a range of distinct time-series to…
Channel formation and branching is widely seen in physical systems where movement of fluid through a porous structure causes the spatiotemporal evolution of the medium in response to the flow, in turn causing flow pathways to evolve. We…
Convergent extension of epithelial tissue is a key motif of animal morphogenesis. On a coarse scale, cell motion resembles laminar fluid flow; yet in contrast to a fluid, epithelial cells adhere to each other and maintain the tissue layer…
A common developmental process, called branching morphogenesis, generates the epithelial trees in a variety of organs, including the lungs, kidneys, and glands. How branching morphogenesis can create epithelial architectures of very…