Related papers: Cellular gradient flow structure connects single-c…
Stem cell heterogeneity is essential for the homeostasis in tissue development. This paper established a general formulation for understanding the dynamics of stem cell regeneration with cell heterogeneity and random transitions of…
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…
Cellular differentiation is governed by gene regulatory networks, the high-dimensional stochastic biochemical systems that determine the transcriptional landscape and mediate cellular responses to signals and perturbations. Although…
To unveil the logic of cell from a level of chemical reaction dynamics, we need to clarify how ensemble of chemicals can autonomously produce the set of chemical, without assuming a specific external control echanism. A cell consists of a…
Disease awareness in infection dynamics can be modeled with adaptive contact networks whose rewiring rules reflect the attempt by susceptibles to avoid infectious contacts. Simulations of this type of models show an active phase with…
We present a simple approach allowing to obtain analytical expressions for laser pulses that can drive a two-level system in an arbitrarily chosen way. The proposed scheme relates every desired population-evolution path to a single resonant…
As cells grow and divide under a given environment, they become crowded and resources are limited, as seen in bacterial biofilms and multicellular aggregates. These cells often show strong interactions through exchanging chemicals, as in…
Cell-to-cell variability is inherent to numerous biological processes, including cell migration. Quantifying and characterizing the variability of migrating cells is challenging, as it requires monitoring many cells for long time windows…
Multimodal single-cell technologies enable the simultaneous collection of diverse data types from individual cells, enhancing our understanding of cellular states. However, the integration of these datatypes and modeling the…
Identity, response to external stimuli, and spatial architecture of a living system are central topics of molecular biology. Presently, they are largely seen as a result of the interplay between a gene repertoire and the regulatory…
Various multicellular tissues show chiral morphology. Experimental studies have shown this can originate from cell chirality. However, no theory has been proposed to connect the cellular chiral torque and multicellular chiral morphogenesis.…
Multicellular organisms contain a wide variety of highly specialized cell types. The consistency and robustness of developmental trajectories suggest that complex gene regulatory networks effectively act as low-dimensional cell fate…
Many cellular processes involve information processing and decision making. We can probe these processes at increasing molecular detail. The analysis of heterogeneous data remains a challenge that requires new ways of thinking about cells…
In previous work, we studied host response to a pathogen which uses a cycle of immunologically distinct stages to establish and maintain infection. We showed that for generic parameter values, the system has a unique biologically meaningful…
We discuss several continuum cell-cell adhesion models based on the underlying microscopic assumptions. We propose an improvement on these models leading to sharp fronts and intermingling invasion fronts between different cell type…
We construct a pathwise formulation for a multi-type age-structured population dynamics, which involves an age-dependent cell replication and transition of gene- or phenotypes. By employing the formulation, we derive a variational…
Understanding and modelling the complexity of the immune system is a challenge that is shared by the ImmunoComplexiT$^1$ thematic network from the RNSC. The immune system is a complex biological, adaptive, highly diversified, self-organized…
A dynamical systems scenario for developmental cell biology is proposed, based on numerical studies of a system with interacting units with internal dynamics and reproduction. Diversification, formation of discrete and recursive types, and…
Flow cytometry is a widespread single-cell measurement technology with a multitude of clinical and research applications. Interpretation of flow cytometry data is hard; the instrumentation is delicate and can not render absolute…
Multicellular organisms exhibit a high degree of structural organization with specific cell types always occurring in characteristic locations. The conventional framework for describing the emergence of such consistent spatial patterns is…