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We study the Stochastic Thermodynamics of cell growth and division using a theoretical framework based on branching processes with resetting. Cell division may be split into two sub-processes: branching, by which a given cell gives birth to…
I consider how cell shape and environmental geometry affect the rate of nutrient capture and the consequent maximum growth rate of a cell, focusing on rod-like species like \textit{E.\ coli}. Simple modeling immediately implies that it is…
We outline a theoretical framework for estimating the evolution of the particle size distribution in colloid and nanoparticle synthesis, when the primary growth mode is by externally controlled addition of singlet building blocks. The…
Microbial colonies cultured on agar Petri dishes have become a model system to study biological evolution in populations expanding in space. Processes such as clonal segregation and gene surfing have been shown to be affected by…
The first and maybe the most important step in designing a model-based predictive controller is to develop a model that is as accurate as possible and that is valid under a wide range of operating conditions. The sugar boiling process is a…
In this work, we introduce Progressive Growing of Patch Size, an automatic curriculum learning approach for 3D medical image segmentation. Our approach progressively increases the patch size during model training, resulting in an improved…
We model the growth of a cell population by a piecewise deterministic Markov branching tree. Each cell splits into two offsprings at a division rate $B(x)$ that depends on its size $x$. The size of each cell grows exponentially in time, at…
Positioning of the midcell division plane within the bacterium E. coli is controlled by the min system of proteins: MinC, MinD and MinE. These proteins coherently oscillate from end to end of the bacterium. We present a reaction--diffusion…
Bacterial colonies can form a wide variety of shapes and structures based on ambient and internal conditions. To help understand the mechanisms that determine the structure of and the diversity within these colonies, various numerical…
Despite the importance that fluid flow plays in transporting and organizing populations, few laboratory systems exist to systematically investigate the impact of advection on their spatial evolutionary dynamics. To address this problem, we…
We study motility-induced phase separation (MIPS) in symmetric and asymmetric active binary mixtures. We start with the coarse-grained run-and-tumble bacterial model that provides evolution equations for the density fields $\rho_i(\vec r,…
We introduce a new coordination problem in distributed computing that we call the population stability problem. A system of agents each with limited memory and communication, as well as the ability to replicate and self-destruct, is…
Inspired by recent developments in neural speech coding and diffusion-based language modeling, we tackle speech enhancement by modeling the conditional distribution of clean speech codes given noisy speech codes using absorbing discrete…
The divide and conquer strategy, which breaks a massive data set into a se- ries of manageable data blocks, and then combines the independent results of data blocks to obtain a final decision, has been recognized as a state-of-the-art…
Collective migration dominates many phenomena, from cell movement in living systems to abiotic self-propelling particles. Focusing on the early stages of tumor evolution, we enunciate the principles involved in cell dynamics and highlight…
The space $\mathcal{G}_n$ of $n$-marked groups provides a natural framework for studying algebraic and geometric invariants under deformation. In general, the growth rate is not continuous on $\mathcal{G}_n$. In this paper, we investigate…
The distributions of many proteins in rod-shaped bacteria are far from homogenous. Often they accumulate at the cell poles or in the cell center. At the same time, the copy number of proteins in a single cell is relatively small making the…
In this article, we discuss the continuous version of the generalized exchange-driven growth model which is a variant of the coagulation model in which a smaller size particle is detached from a bigger one and merges with another particle.…
This paper theoretically analyzes a phenomenological stochastic model for bacterial growth. This model comprises cell division and the linear growth of cells, where growth rates and cell cycles are drawn from lognormal distributions. We…
As a population grows, spreading to new environments may favor specialization. In this paper, we introduce and explore a model for specialization at the front of a colony expanding synchronously into new territory. We show through numerical…