相关论文: Real-time Evolution of Multicellularity with Artif…

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…

A properly designed controller can help improve the quality of experimental measurements or force a dynamical system to follow a completely new time-evolution path. Recent developments in deep reinforcement learning have made steep advances…

The complexity of gene regulatory networks in multicellular organisms makes interpretable low-dimensional models highly desirable. An attractive geometric picture, attributed to Waddington, visualizes the differentiation of a cell into…

All life, including cells and artificial protocells, must integrate diverse molecules into a single unit in order to reproduce. Despite expected pressure to evolve a simple system with the fastest replication speed, the mechanism by which…

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…

The evolution of complex cellular life involved two major transitions: the encapsulation of self-replicating genetic entities into cellular units and the aggregation of individual genes into a collectively replicating genome. In this paper,…

How can a microorganism adapt to a variety of environmental conditions despite there exists a limited number of signal transduction machineries? We show that for any growing cells whose gene expression is under stochastic fluctuations,…

BioDynaMo is a biological processes simulator developed by an international community of researchers and software engineers working closely with neuroscientists. The authors have been working on gene expression, i.e. the process by which…

The organization of live cells to tissues is associated with the mechanical interaction between cells, which is mediated through their elastic environment. We model cells as spherical active force dipoles surrounded by an infinite elastic…

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…

A one-dimensional cellular automaton with a probabilistic evolution rule can generate stochastic surface growth in $(1 + 1)$ dimensions. Two such discrete models of surface growth are constructed from a probabilistic cellular automaton…

Neural Cellular Automata (NCAs) are a model of morphogenesis, capable of growing two-dimensional artificial organisms from a single seed cell. In this paper, we show that NCAs can be trained to respond to signals. Two types of signal are…

Replication time is among the most important components of a bacterial cell's reproductive fitness. Paradoxically, larger cells replicate in less time than smaller cells despite the fact that building a larger cell requires increased…

The applicability of computational and dynamical systems models to organisms is scrutinized, using examples from developmental biology and cognition. Developmental morphogenesis is dependent on the inherent material properties of developing…

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…

Living organisms rely on endogenous feedback mechanisms to maintain homeostasis in the presence of uncertainty and environmental fluctuations. An emerging challenge at the interface of control systems engineering and synthetic biology is…

Spatial self-organization emerges in distributed systems exhibiting local interactions when nonlinearities and the appropriate propagation of signals are at work. These kinds of phenomena can be modeled with different frameworks, typically…

Understanding the emergence and evolution of multicellularity and cellular differentiation is a core problem in biology. We develop a quantitative model that shows that a multicellular form emerges from genetically identical unicellular…

During developmental processes such as embryogenesis, how a group of cells fold into specific structures, is a central question in biology that defines how living organisms form. Establishing tissue-level morphology critically relies on how…

Cellular decision-making based on information received from the external environment is frequently initiated by transmembrane receptors. These receptors are known to propagate such information by triggering a series of irreversible,…