Related papers: A mechanistic first--passage time framework for ba…
Even in large systems, the effect of noise arising from when populations are initially small can persist to be measurable on the macroscale. A deterministic approximation to a stochastic model will fail to capture this effect, but it can be…
In proliferating cell populations, adaptive changes to biochemical reactions can change a cell's division time, which in turn can change the population size. However, biochemical reactions are subject to noise, and therefore the conditions…
We describe a continuous-time modelling framework for biological population dynamics that accounts for demographic noise. In the spirit of the methodology used by statistical physicists, transitions between the states of the system are…
Gene expression in individual cells is highly variable and sporadic, often resulting in the synthesis of mRNAs and proteins in bursts. Bursting in gene expression is known to impact cell-fate in diverse systems ranging from latency in HIV-1…
Finding the most powerful node in a dynamic random network, the largest set in a partition-valued stochastic process, or the largest family in an evolving population at a given time, can be a very difficult problem. This is particularly the…
We present a study of disorder origination and growth inside an ordered phase processes induced by the presence of multiplicative noise within mean-field approximation. Our research is based on the study of solutions of the nonlinear…
Size segregation in bedload transport is studied numerically with a coupled fluid-discrete element model. Starting from an initial deposit of small spherical particles on top of a large particle bed, the segregation dynamics of the bed is…
Constraints on changes in expression levels across all cell components imposed by the steady growth of cells have recently been discussed both experimentally and theoretically. By assuming a small environmental perturbation and considering…
It has been proposed that during the early steps in the origin of life, small droplets could have formed via the segregation of molecules from complex mixtures by phase separation. These droplets could have provided chemical reaction…
We present feature finding and tracking algorithms in 3D in living cells, and demonstrate their utility to measure metrics important in cell biological processes. We developed a computational imaging hybrid approach that combines automated…
We derive the full kinetic equations describing the evolution of the probability density distribution for a structured population such as cells distributed according to their ages and sizes. The kinetic equations for such a "sizer-timer"…
To describe the nonequilibrium states of a system we introduce a new thermodynamic parameter - the lifetime (the first passage time) of a system. The statistical distributions that can be obtained out of the mesoscopic description…
Mathematical models are vital interpretive and predictive tools used to assist in the understanding of cell migration. There are typically two approaches to modelling cell migration: either micro-scale, discrete or macro-scale, continuum.…
Most microorganisms regulate their cell size. We review here some of the mathematical formulations of the problem of cell size regulation. We focus on coarse-grained stochastic models and the statistics they generate. We review the…
For proliferating cells subject to both division and death, how can one estimate the average generation number of the living population without continuous observation or a division-diluting dye? In this paper we provide a method for cell…
The dynamics of cellular aggregates is driven by the interplay of mechanochemical processes and cellular activity. Although deterministic models may capture mechanical features, local chemical fluctuations trigger random cell responses,…
Biological cells replicate their genomes in a well-planned manner. The DNA replication program of an organism determines the timing at which different genomic regions are replicated, with fundamental consequences for cell homeostasis and…
Cell proliferation is typically incorporated into stochastic mathematical models of cell migration by assuming that cell divisions occur after an exponentially distributed waiting time. Experimental observations, however, show that this…
Cellular behaviors such as migration, division, and differentiation rely on precise timing, and yet the molecular events that govern these behaviors are highly stochastic. We investigate regulatory strategies that decrease the timing noise…
Aging, the dependence of the dynamics of a physical process on the time $t_a$ since its original preparation, is observed in systems ranging from the motion of charge carriers in amorphous semiconductors over the blinking dynamics of…