Related papers: Cellular gradient flow structure connects single-c…
In multicellular organisms, several cell states coexist. For determining each cell type, cell-cell interactions are often essential, in addition to intracellular gene expression dynamics. Based on dynamical systems theory, we propose a…
Continuum models for the spatial dynamics of growing cell populations have been widely used to investigate the mechanisms underpinning tissue development and tumour invasion. These models consist of nonlinear partial differential equations…
A big challenge in current biology is to understand the exact self-organization mechanism underlying complex multi-physics coupling developmental processes. With multiscale computations of from subcellular gene expressions to cell…
One of the many ways cells transmit information within their volume is through steady spatial gradients of different proteins. However, the mechanism through which proteins without any sources or sinks form such single-cell gradients is not…
Single-cell experiments have revealed cell-to-cell variability in generation times and growth rates for genetically identical cells. Theoretical models relating the fluctuating generation times of single cells to the population growth rate…
A dynamic model for cell differentiation is studied, where cells with internal chemical reaction dynamics interact with each other and replicate. It leads to spontaneous differentiation of cells and determination, as is discussed in the…
We propose a modelling framework to analyse the stochastic behaviour of heterogeneous, multi-scale cellular populations. We illustrate our methodology with a particular example in which we study a population with an oxygen-regulated…
Cells coexist together in colonies or as tissues. Their behaviour is controlled by an interplay between intercellular forces and biochemical regulation. We develop a simple model of the cell cycle, the fundamental regulatory network…
A rigorous understanding of how multicellular behaviors arise from the actions of single cells requires quantitative frameworks that bridge the gap between genetic circuits, the arrangement of cells in space, and population-level behaviors.…
Living systems, particularly multicellular systems, often seem hopelessly complex. But recent studies have suggested that beneath this complexity, there may be unifying quantitative principles that we are only now starting to unravel. All…
Basic problems for the construction of a scenario for the Life are discussed. To study the problems in terms of dynamical systems theory, a scheme of intra-inter dynamics is presented. It consists of internal dynamics of a unit, interaction…
Establishing a quantitative connection between the population growth rate and the generation times of single cells is a prerequisite for understanding evolutionary dynamics of microbes. However, existing theories fail to account for the…
How are granular details of stochastic growth and division of individual cells reflected in smooth deterministic growth of population numbers? We provide an integrated, multiscale perspective of microbial growth dynamics by formulating a…
A cell's behavior is a consequence of the complex interactions between its numerous constituents, such as DNA, RNA, proteins and small molecules. Cells use signaling pathways and regulatory mechanisms to coordinate multiple processes,…
Dynamics maintaining diversity of cell types in a multi-cellular system are studied in relationship with the plasticity of cellular states. First, we introduce a new theoretical framework, reaction-diffusion system on `chemical species…
Gradient-based learning in multi-layer neural networks displays a number of striking features. In particular, the decrease rate of empirical risk is non-monotone even after averaging over large batches. Long plateaus in which one observes…
Multicellular organisms comprise a diverse collection of stable tissues built from different cell types. It remains unclear how large numbers of interacting cells can precisely coordinate their gene expression during tissue…
We introduce and analyze several aspects of a new model for cell differentiation. It assumes that differentiation of progenitor cells is a continuous process. From the mathematical point of view, it is based on partial differential…
Dynamics maintaining diversity of cell types in a multi-cellular system are studied in relationship with the plasticity of cellular states. By adopting a simple theoretical framework for intra-cellular chemical reaction dynamics with…
Stem cell regeneration is a vital biological process in self-renewing tissues, governing development and tissue homeostasis. Gene regulatory network dynamics are pivotal in controlling stem cell regeneration and cell type transitions.…