Related papers: Learning developmental mode dynamics from single-c…
The quintessential property of neuronal systems is their intensive patterns of selective synaptic connections. The current work describes a physics-based approach to neuronal shape modeling and synthesis and its consideration for the…
Neural development represents not only an exciting and complex field of study, with ongoing progress, but it also became the epicentre of neuroscience and developmental biology, as it strives to describe the underlying cellular and…
Stem cell regeneration is a crucial biological process for most self-renewing tissues during the development and maintenance of tissue homeostasis. In developing the mathematical models of stem cell regeneration and tissue development, cell…
Cell proliferation and cell movement are fundamentally stochastic processes which lead to variability in the growth and spatial structure of cell populations in many biological settings, such as cell invasion, wound healing, and tumour…
In proliferating epithelia of mammalian skin, cells of irregular polygonal-like shapes pack into complex nearly flat two-dimensional structures that are pliable to deformations. In this work, we employ various sensitive correlation…
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…
A continuum model of epithelial tissue mechanics was formulated using cellular-level mechanical ingredients and cell morphogenetic processes, including cellular shape changes and cellular rearrangements. This model can include finite…
Different subsystems of organisms adapt over many time scales, such as rapid changes in the nervous system (learning), slower morphological and neurological change over the lifetime of the organism (postnatal development), and change over…
We introduce a model for describing the dynamics of large numbers of interacting cells. The fundamental dynamical variables in the model are sub-cellular elements, which interact with each other through phenomenological intra- and…
Uncovering the rules governing the nonequilibrium dynamics of the membranes that define biological cells is of central importance to understanding the physics of living systems. We theoretically and computationally investigate the behavior…
Bulk tissue RNA sequencing of heterogeneous samples provides averaged gene expression profiles, obscuring cell type-specific dynamics. To address this, we present a probabilistic hierarchical Bayesian model that deconvolves bulk RNA-seq…
The initiation of directional cell motion requires symmetry breaking that can happen both with or without external stimuli. During cell crawling, forces generated by the cytoskeleton and their transmission through mechanosensitive adhesions…
Many fundamental biological processes are dependent on cellular migration. Although the mechanical mechanisms of single-cell migration are relatively well understood, those underlying migration of multiple cells adhered to each other in a…
We propose a three dimensional mechanical model of embryonic tissue dynamics. Mechanically coupled adherent cells are represented as particles interconnected with elastic beams which can exert non-central forces and torques. Tissue…
We formulate a general, high-dimensional kinetic theory describing the internal state (such as gene expression or protein levels) of cells in a stochastically evolving population. The resolution of our kinetic theory also allows one to…
We present a COMSOL Multiphysics implementation of a continuum model for directed cell migration, a key mechanism underlying tissue self-organization and morphogenesis. The model is formulated as a partial integro-differential equation…
Diffusion and flow matching approaches to generative modeling have shown promise in domains where the state space is continuous, such as image generation or protein folding & design, and discrete, exemplified by diffusion large language…
A series of simulations aimed at elucidating the self-assembly dynamics of spherical virus capsids is described. This little-understood phenomenon is a fascinating example of the complex processes that occur in the simplest of organisms.…
Swarming or collective motion of living entities is one of the most common and spectacular manifestations of living systems having been extensively studied in recent years. A number of general principles have been established. The…
Recent whole brain imaging experiments on $\textit{C. elegans}$ has revealed that the neural population dynamics encode motor commands and stereotyped transitions between behaviors on low dimensional manifolds. Efforts to characterize the…