Related papers: Geometrical constraints in a gene network model an…
The topology of many real complex networks has been conjectured to be embedded in hidden metric spaces, where distances between nodes encode their likelihood of being connected. Besides of providing a natural geometrical interpretation of…
Proteins control many vital functions in living cells, such as cell growth and cell division. Reliable coordination of these functions requires the spatial and temporal organizaton of proteins inside cells, which encodes information about…
Gene regulatory networks play a crucial role in controlling an organism's biological processes, which is why there is significant interest in developing computational methods that are able to extract their structure from high-throughput…
The migratory dynamics of cells can be influenced by the complex micro-environment through which they move. It remains unclear how the motility machinery of confined cells responds and adapts to their micro-environment. Here, we propose a…
We develop a geometric framework to study the structure and function of complex networks. We assume that hyperbolic geometry underlies these networks, and we show that with this assumption, heterogeneous degree distributions and strong…
During organismal development, biochemical reaction networks sense and respond to mechanical forces to coordinate embryonic patterning with embryo morphogenesis. Factors such as cortical tension, cell density, and matrix mechanical…
Brain networks exhibit remarkable structural properties, including high local clustering, short path lengths, and heavy-tailed weight and degree distributions. While these features are thought to enable efficient information processing with…
Mechanical product engineering often must comply with manufacturing or geometric constraints related to the shaping process. Mechanical design hence should rely on robust and fast tools to explore complex shapes, typically for design for…
Understanding how biological constraints shape neural computation is a central goal of computational neuroscience. Spatially embedded recurrent neural networks provide a promising avenue to study how modelled constraints shape the combined…
Background: Duplication of genes is important for evolution of molecular networks. Many authors have therefore considered gene duplication as a driving force in shaping the topology of molecular networks. In particular it has been noted…
Brain morphology is shaped by genetic and mechanical factors and is linked to biological development and diseases. Its fractal-like features, regional anisotropy, and complex curvature distributions hinder quantitative insights in medical…
Statistical learning in high-dimensional spaces is challenging without a strong underlying data structure. Recent advances with foundational models suggest that text and image data contain such hidden structures, which help mitigate the…
Geometric and structural constraints greatly restrict the selection of folds adapted by protein backbones, and yet, folded proteins show an astounding diversity in functionality. For structure to have any bearing on function, it is thus…
We consider evolution of a large population, where fitness of each organism is defined by many phenotypical traits. These traits result from expression of many genes. We propose a new model of gene regulation, where gene expression is…
Genetic regulatory networks enable cells to respond to the changes in internal and external conditions by dynamically coordinating their gene expression profiles. Our ability to make quantitative measurements in these biochemical circuits…
Recurrent neural networks are frequently studied in terms of their information-processing capabilities. The structural properties of these networks are seldom considered, beyond those emerging from the connectivity tuning necessary for…
Transport in crowded, complex environments occurs across many spatial scales. Geometric restrictions can hinder the motion of individuals and, combined with crowding between individuals, can have drastic effects on global transport…
Intracellular protein patterns regulate a variety of vital cellular processes such as cell division and motility, which often involve dynamic changes of cell shape. These changes in cell shape may in turn affect the dynamics of…
Genetic regulation is a key component in development, but a clear understanding of the structure and dynamics of genetic networks is not yet at hand. In this work we investigate these properties within an artificial genome model originally…
Diffusion-driven instability is a fundamental mechanism underlying pattern formation in spatially extended systems. In almost all existing works, diffusion across the links of the underlying network is modeled through scalar weights,…