相关论文: An explanatory evo-devo model for the developmenta…

Macroscopic, phenomenological models have proven useful as concise framings of our understandings in fields from statistical physics to economics to biology. Constructing a phenomenological model for development would provide a framework…

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…

We introduce a model, based on the Evolutionary Game Theory, for studying the dynamics of group formation. The latter constitutes a relevant phenomenon observed in different animal species, whose individuals tend to cluster together forming…

We show that the Tangled Nature model can be interpreted as a general formulation of the quasi-species model by Eigen et al. in a frequency dependent fitness landscape. We present a detailed theoretical derivation of the mutation threshold,…

Several populational networks present complex topologies when implemented in evolutionary algorithms. A common feature of these topologies is the emergence of a power law. Power law behavior with different scaling factors can also be…

Specific activator and repressor transcription factors which bind to specific regulator DNA sequences, play an important role in gene activity control. Interactions between genes coding such transcription factors should explain the…

The evolution of high-dimensional phenotypes is investigated using a statistical physics model consists of interacting spins, in which genotypes, phenotypes, and environments are represented by spin configurations, interaction matrices, and…

Timing is essential for many cellular processes, from cellular responses to external stimuli to the cell cycle and circadian clocks. Many of these processes are based on gene expression. For example, an activated gene may be required to…

Aging is thought to be a consequence of intrinsic breakdowns in how genetic information is processed. But mounting experimental evidence suggests that aging can be slowed. To help resolve this mystery, I derive a mortality equation which…

Many experiments have been performed that use evolutionary algorithms for learning the topology and connection weights of a neural network that controls a robot or virtual agent. These experiments are not only performed to better understand…

Grammatical forms are said to evolve via two main mechanisms. These are, respectively, the `descent' mechanism, where current forms can be seen to have descended (albeit with occasional modifications) from their roots in ancient languages,…

Methods for time series prediction and classification of gene regulatory networks (GRNs) from gene expression data have been treated separately so far. The recent emergence of attention-based recurrent neural networks (RNN) models boosted…

We investigate the evolutionary dynamics of an idealised model for the robust self-assembly of two-dimensional structures called polyominoes. The model includes rules that encode interactions between sets of square tiles that drive the…

Self-regulatory models are common in nature, as described e.g. in (\cite{mur}), (\cite{ha}) and (\cite{Gb}).\\ Let us consider a system made up of a number of glands as a motivation. Each gland secretes a hormone that allows secretion in…

Structural and dynamical fingerprints of evolutionary optimization in biological networks are still unclear. We here analyze the dynamics of genetic regulatory networks responsible for the regulation of cell cycle and cell differentiation…

Mathematical models play an increasingly important role in the interpretation of biological experiments. Studies often present a model that generates the observations, connecting hypothesized process to an observed pattern. Such generative…

The concept of fitness is central to evolution, but it quantifies only the expected number of offspring an individual will produce. The actual number of offspring is also subject to noise, arising from environmental or demographic…

A common metaphor for describing development is a rugged "epigenetic landscape" where cell fates are represented as attracting valleys resulting from a complex regulatory network. Here, we introduce a framework for explicitly constructing…

During tissue development, patterns of gene expression determine the spatial arrangement of cell types. In many cases, gradients of secreted signaling molecules - morphogens - guide this process. The continuous positional information…

A model for morphoelastic growth, that is, growth influenced by elastic stress, driven by the absorption of nutrients is considered. The model features a multiplicative decomposition of the deformation gradient into an elastic contribution…