Related papers: Relevant parameters in models of cell division con…
A packed community of exponentially proliferating microbes will spread in size exponentially. However, due to nutrient depletion, mechanical constraints, or other limitations, exponential proliferation is not indefinite, and the spreading…
The understanding of morphogenesis in living organisms has been renewed by tremendous progressin experimental techniques that provide access to cell-scale, quantitative information both on theshapes of cells within tissues and on the genes…
Single-cell data provide high-dimensional measurements of the transcriptional states of cells, but extracting insights into the regulatory functions of genes, particularly identifying transcriptional mechanisms affected by biological…
The first chapter concerns monotype population models. We first study general birth and death processes and we give non-explosion and extinction criteria, moment computations and a pathwise representation. We then show how different scales…
We study the mathematical properties of a general model of cell division structured with several internal variables. We begin with a simpler and specific model with two variables, we solve the eigenvalue problem with strong or weak…
The movement of intracellular cargo transported by molecular motors is commonly marked by switches between directed motion and stationary pauses. The predominant measure for assessing movement is effective diffusivity, which predicts the…
A simulation approach to the stochastic growth of bacterial towers is presented, in which a non-uniform and finite nutrient supply essentially determines the emerging structure through elementary chemotaxis. The method is based on cellular…
Glycemic regulation is often described as maintaining glucose levels near a stable baseline. However, continuous glucose monitoring after meals displays intra-individual variability even under controlled conditions, suggesting intrinsic…
A connection is established between discrete stochastic model describing microscopic motion of fluctuating cells, and macroscopic equations describing dynamics of cellular density. Cells move towards chemical gradient (process called…
Biophysical models describing complex, cellular phenomena typically include systems of nonlinear differential equations with many free parameters. While experimental measurements can fix some parameters, those describing internal cellular…
The effect of mechanical interactions between cells in the spreading of bacterial populations was investigated in one-dimensional space. A continuum-mechanics approach, comprising cell migration, proliferation, and exclusion processes, was…
Within a continuous-time, stochastic model of single-cell size homeostasis, we study how the structure of feedback from size to growth rates and cell-cycle progression shapes overall size dynamics, both within and across cell cycles. We…
Cell size control is crucial for maintaining cellular function and homeostasis. In this study, we develop a first-order partial differential equation model to examine the effects of three key size control mechanisms: the sizer, timer, and…
Subdiffusion has been proposed as an explanation of various kinetic phenomena inside living cells. In order to fascilitate large-scale computational studies of subdiffusive chemical processes, we extend a recently suggested mesoscopic model…
To forecast the time dynamics of an epidemic, we propose a discrete stochastic model that unifies and generalizes previous approaches to the subject. Viewing a given population of individuals or groups of individuals with given health state…
Multipotent stem or progenitor cells undergo a sequential series of binary fate decisions, which ultimately generate the diversity of differentiated cells. Efforts to understand cell fate control have focused on simple gene regulatory…
The transmission dynamics of an epidemic are rarely homogeneous. Super-spreading events and super-spreading individuals are two types of heterogeneous transmissibility. Inference of super-spreading is commonly carried out on secondary case…
Spatial profiling technologies in biology, such as imaging mass cytometry (IMC) and spatial transcriptomics (ST), generate high-dimensional, multi-channel data with strong spatial alignment and complex inter-channel relationships.…
Scale independence is a ubiquitous feature of complex systems which implies a highly skewed distribution of resources with no characteristic scale. Research has long focused on why systems as varied as protein networks, evolution and stock…
The self-organization of proteins into enriched compartments and the formation of complex patterns are crucial processes for life on the cellular level. Liquid-liquid phase separation is one mechanism for forming such enriched compartments.…