Related papers: Morphogenesis by coupled regulatory networks

Molecular noise in gene regulatory networks has two intrinsic components, one part being due to fluctuations caused by the birth and death of protein or mRNA molecules which are often present in small numbers and the other part arising from…

Learning and decision making in the brain are key processes critical to survival, and yet are processes implemented by non-ideal biological building blocks which can impose significant error. We explore quantitatively how the brain might…

This paper introduces a continuous model for Multi-cellular Developmental Design. The cells are fixed on a 2D grid and exchange "chemicals" with their neighbors during the growth process. The quantity of chemicals that a cell produces, as…

The processes of gene expression are inherently stochastic, even for essential genes required for growth. How does the cell maximize fitness in light of noise? To answer this question, we build a mathematical model to explore the trade-off…

Control of nonlinear large-scale dynamical networks, e.g., collective behavior of agents interacting via a scale-free connection topology, is a central problem in many scientific and engineering fields. For the linear version of this…

Morphogenesis in the central nervous system has received intensive attention as elucidating fundamental mechanisms of morphogenesis will shed light on the physiology and pathophysiology of the developing central nervous system.…

We study the dynamics of flow-networks in porous media using a pore-network model. First, we consider a class of erosion dynamics assuming a constitutive law depending on flow rate, local velocities, or shear stress at the walls. We show…

Adaptive control in biological systems, such as intestinal immunity, remains poorly understood despite detailed knowledge of underlying regulatory networks. We propose an alternative framework based on stochastic martingale turnover, in…

Diffusion models generate structure by progressively transforming noise into data, yet the mechanisms underlying this transition remain poorly understood. In this work, we show that pattern formation in trained diffusion models can be…

Theoretical descriptions of the stepping-stone model, a cornerstone of spatial population genetics, have long overlooked diffusive noise arising from migration dynamics. We derive an exact fluctuating hydrodynamic description of this model…

There is a growing body of work considering the use of representations based upon genetic regulatory networks. This paper uses a recently presented abstract, tunable Boolean regulatory network model to explore aspects of mobile DNA, such as…

Dynamic gene-regulatory networks are complex since the number of potential components involved in the system is very large. Estimating dynamic networks is an important task because they compromise valuable information about interactions…

Neuronal networks constitute a special class of dynamical systems, as they are formed by individual geometrical components, namely the neurons. In the existing literature, relatively little attention has been given to the influence of…

Dimension reduction is a common strategy to study non-linear dynamical systems composed by a large number of variables. The goal is to find a smaller version of the system whose time evolution is easier to predict while preserving some of…

We analyze the macroscopic behavior of multi-populations randomly connected neural networks with interaction delays. Similar to cases occurring in spin glasses, we show that the sequences of empirical measures satisfy a large deviation…

We study the effect of correlations in generation times on the dynamics of population growth of microorganisms. We show that any non-zero correlation that is due to cell-size regulation, no matter how small, induces long-term oscillations…

Multidimensional systems coupled via complex networks are widespread in nature and thus frequently invoked for a large plethora of interesting applications. From ecology to physics, individual entities in mutual interactions are grouped in…

The membrane components of cellular organelles have been shown to segregate into domains as the result of biochemical maturation. We propose that the dynamical competition between maturation and lateral segregation of membrane components…

Two-dimensional shape-morphing networks are common in biological systems and have garnered attention due to their nontrivial physical properties that emanate from their cellular nature. Here, we present the fabrication and characterization…

From the smallest biological systems to the largest cosmological structures, spatial domains undergo expansion and contraction. Within these growing domains, diffusive transport is a common phenomenon. Mathematical models have been widely…