Related papers: Non-genetic heterogeneity criticality and cell dif…
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…
Stem cells, through their ability to produce daughter stem cells and differentiate into specialized cells, are essential in the growth, maintenance, and repair of biological tissues. Understanding the dynamics of cell populations in the…
Eukaryotic gene regulation is based on stochastic yet controlled promoter switching, during which genes transition between transcriptionally active and inactive states. Despite the molecular complexity of this process, recent studies reveal…
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…
Formulating quantitative and predictive models for tissue development requires consideration of the complex, stochastic gene expression dynamics, its regulation via cell-to-cell interactions, and cell proliferation. Including all of these…
The intrinsic stochasticity of gene expression can lead to large variability of protein levels across a population of cells. Variability (or noise) in protein distributions can be modulated by cellular mechanisms of gene regulation; in…
The observation that phenotypic variability is ubiquitous in isogenic populations has led to a multitude of experimental and theoretical studies seeking to probe the causes and consequences of this variability. Whether it be in the context…
We derive exact solutions of simplified models for the temporal evolution of the protein concentration within a cell population arbitrarily far from the stationary state. We show that monitoring the dynamics can assist in modeling and…
Gene expression is a central process to any form of life. It involves multiple temporal and functional scales that extend from specific protein-DNA interactions to the coordinated regulation of multiple genes in response to intracellular…
It is becoming increasingly appreciated that the signal transduction systems used by eukaryotic cells to achieve a variety of essential responses represent highly complex networks rather than simple linear pathways. While significant effort…
We investigate proteins within heterogeneous cell membranes where non-equilibrium phenomena arises from spatial variations in concentration and temperature. We develop simulation methods building on non-equilibrium statistical mechanics to…
According to recent experimental evidence, the architecture of a promoter, defined as the number, strength and regulatory role of the operators that control the promoter, plays a major role in determining the level of cell-to-cell…
Based on a recently proposed non-equilibrium mechanism for spatial pattern formation [cond-mat/0312366] we study how morphogenesis can be controlled by locally coupled discrete dynamical networks, similar to gene regulation networks of…
The fundamental biological processes of development of tissues and organs in multicellular organisms is governed by various signaling molecules, which are called morphogens. It is known that spatial and temporal variations in concentration…
For the first time the phenomenon of cellular structure coarsening are consistently analysed from the positions of kinetic, hydrodynamic and stochastodynamic theories of nonequilibrium statistical systems. Thereby micro-, meso- and…
Stochastic oscillations in individual cells are usually characterized by a non-monotonic power spectrum with an oscillatory autocorrelation function. Here we develop an analytical approach of stochastic oscillations in a minimal hybrid…
For the past few years, deep generative models have increasingly been used in biological research for a variety of tasks. Recently, they have proven to be valuable for uncovering subtle cell phenotypic differences that are not directly…
Chromatin remodeling machineries are abundant and diverse in eukaryotic cells. They have been involved in a variety of situations such as histone exchange and DNA repair, but their importance in gene expression remains unclear. Although the…
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…
Through extensive studies of dynamical system modeling cellular growth and reproduction, we find evidence that complexity arises in multicellular organisms naturally through evolution. Without any elaborate control mechanism, these systems…