Related papers: Cell decision-making through the lens of Bayesian …
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…
Animal morphogenesis often involves significant shape changes of epithelial tissue sheets. Great progress has been made in understanding the underlying cellular driving forces and their coordination through biomechanical feedback loops.…
The brain is a biological system comprising nerve cells and orchestrates its embodied agent's perception, behavior, and learning in the dynamic environment. The free energy principle (FEP) advocated by Karl Friston explicates the local,…
Cells generally change their internal state to adapt to an environmental change, and accordingly evolve in response to the new conditions. This process involves phenotypic changes that occur over several different time scales, ranging from…
We study a dynamic model of Bayesian persuasion in sequential decision-making settings. An informed principal observes an external parameter of the world and advises an uninformed agent about actions to take over time. The agent takes…
Optimization-based models have been used to predict cellular behavior for over 25 years. The constraints in these models are derived from genome annotations, measured macro-molecular composition of cells, and by measuring the cell's growth…
Intracellular protein patterns govern essential cellular functions by dynamically redistributing proteins between membrane-bound and cytosolic states, conserving their total numbers. This review presents a theoretical framework for…
Communication between cells is realized by exchange of biochemical substances. Due to internal organization of living systems and variability of external parameters, the exchange is heavily influenced by perturbations of various parameters…
Tissue homeostasis, the biological process of maintaining a steady state in tissue via control of cell proliferation, death, and metabolic function, is essential for the development, growth, maintenance, and proper function of living…
Pattern formation often occurs in confined systems, yet how boundaries shape patterning dynamics is unclear. We develop techniques to analyze confinement effects in nonlocal advection-diffusion equations, which generically capture the…
Developing reliable mechanisms for continuous local learning is a central challenge faced by biological and artificial systems. Yet, how the environmental factors and structural constraints on the learning network influence the optimal…
Every interaction of a living organism with its environment involves the placement of a bet. Armed with partial knowledge about a stochastic world, the organism must decide its next step or near-term strategy, an act that implicitly or…
Markovian population models are suitable abstractions to describe well-mixed interacting particle systems in situation where stochastic fluctuations are significant due to the involvement of low copy particles. In molecular biology,…
We propose a physical model for developmental process at cellular level to discuss the mechanism of epigenetic landscape. In our simplified model, a minimal model, the network of the interaction among cells generates the landscape…
Biological cells encode information about their environment through biochemical signaling networks that control their internal state and response. This information is often encoded in the dynamical patterns of the signaling molecules,…
Group decisions involve the combination of evidence accumulation by individual members and direct member-to-member interactions. We consider a simplified framework of two deciders, each undergoing a two alternative forced choice task, with…
Density dependence is important in the ecology and evolution of microbial and cancer cells. Typically, we can only measure net growth rates, but the underlying density-dependent mechanisms that give rise to the observed dynamics can…
Coordinated responses to environmental stimuli are critical for multicellular organisms. To overcome the obstacles of cell-to-cell heterogeneity and noisy signaling dynamics within individual cells, cells must effectively exchange…
In contexts ranging from embryonic development to bacterial ecology, cell populations migrate chemotactically along self-generated chemical gradients, often forming a propagating front. Here, we theoretically show that the stability of such…
This thesis focuses on three fundamental aspects of biological systems; namely, entropy production, Bayesian mechanics, and the free-energy principle. The contributions are threefold: 1) We compute the entropy production for a greater class…