Related papers: A geometrical perspective on development
Plasticity-led evolution is a form of evolution where a change in the environment induces novel traits via phenotypic plasticity, after which the novel traits are genetically accommodated over generations under the novel environment. This…
Rapid advance of experimental techniques provides an unprecedented in-depth view into complex developmental processes. Still, little is known on how the complexity of multicellular organisms evolved by elaborating developmental programs and…
Development in multi-cellular organisms is marked by a high degree of spatial organization of the cells attaining distinct fates in the embryo. We show that receptor-ligand interaction between cells in close physical proximity adaptively…
Gene Regulatory Network (GRN) plays an important role in knowing insight of cellular life cycle. It gives information about at which different environmental conditions genes of particular interest get over expressed or under expressed.…
We introduce a formalism for the geometry of eukaryotic cells and organisms.Cells are taken to be star-convex with good biological reason. This allows for a convenient description of their extent in space as well as all manner of cell…
Many real-world networks describe systems in which interactions decay with the distance between nodes. Examples include systems constrained in real space such as transportation and communication networks, as well as systems constrained in…
The two most fundamental processes describing change in biology, development and evolu-tion, occur over drastically different timescales, difficult to reconcile within a unified framework. Development involves temporal sequences of cell…
Neural representations of 3D data have been widely adopted across various applications, particularly in recent work leveraging coordinate-based networks to model scalar or vector fields. However, these approaches face inherent challenges,…
Statistical physics provides a useful perspective for the analysis of many complex systems; it allows us to relate microscopic fluctuations to macroscopic observations. Developmental biology, but also cell biology more generally, are…
Understanding how gene regulatory networks (GRNs) give rise to stable and dynamic cellular states remains a central challenge in theoretical biology, particularly when slow epigenetic feedback reshapes the underlying regulatory landscape.…
Networks of gene regulation govern morphogenesis, determine cell identity and regulate cell function. But we have little understanding, at the local level, of which logics are biologically preferred or even permitted. To solve this puzzle,…
A molecule's geometry, also known as conformation, is one of a molecule's most important properties, determining the reactions it participates in, the bonds it forms, and the interactions it has with other molecules. Conventional…
Ordered polarity alignment of a cell population plays a vital role in biology, such as in hair follicle alignment and asymmetric cell division. Here, we propose a theoretical framework for the understanding of generic dynamical properties…
Based on a non-equilibrium mechanism for spatial pattern formation we study how position information can be controlled by locally coupled discrete dynamical networks, similar to gene regulation networks of cells in a developing…
Evolution and geometry generate complexity in similar ways. Evolution drives natural selection while geometry may capture the logic of this selection and express it visually, in terms of specific generic properties representing some kind of…
We typically think of cells as responding to external signals independently by regulating their gene expression levels, yet they often locally exchange information and coordinate. Can such spatial coupling be of benefit for conveying…
This short paper presents an abstract, tunable model of genomic structural change within the cell lifecycle and explores its use with simulated evolution. A well-known Boolean model of genetic regulatory networks is extended to include…
The capacity of cells and organisms to respond to challenging conditions in a repeatable manner is limited by a finite repertoire of pre-evolved adaptive responses. Beyond this capacity, cells can use exploratory dynamics to cope with a…
From the response to external stimuli to cell division and death, the dynamics of living cells is based on the expression of specific genes at specific times. The decision when to express a gene is implemented by the binding and unbinding…
Gene regulatory networks typically have low in-degrees, whereby any given gene is regulated by few of the genes in the network. What mechanisms might be responsible for these low in-degrees? Starting with an accepted framework of the…