Related papers: Branching random tessellations with interaction: A…
The life of a cell is governed by highly dynamical microscopic processes. Two notable examples are the diffusion of membrane receptors and the kinetics of transcription factors governing the rates of gene expression. Different fluorescence…
We analyze evolutionary dynamics in a confluent, branching cellular population, such as in a growing duct, vasculature, or in a branching microbial colony. We focus on the coarse-grained features of the evolution and build a statistical…
Bootstrap percolation is a type of cellular automaton on graphs, introduced as a simple model of the dynamics of ferromagnetism. Vertices in a graph can be in one of two states: `healthy' or `infected' and from an initial configuration of…
Clustering and dependence are common in trials. For example, in some cluster randomized trials (CRTs), pre-existing clusters are enrolled, randomized, and serve as the basis of intervention delivery. Such CRTs are "fully clustered":…
{\it Transcription} is the process whereby RNA molecules are polymerized by molecular machines, called RNA polymerase (RNAP), using the corresponding DNA as the template. Recent {\it in-vivo} experiments with single cells have established…
Simulated Tempering (ST) is an MCMC algorithm for complex target distributions that operates on a path between the target and a more amenable reference distribution. Crucially, if the reference enables i.i.d. sampling, ST is regenerative…
Time-fluctuating signals are ubiquitous and diverse in many physical, chemical, and biological systems, among which random telegraph signals (RTSs) refer to a series of instantaneous switching events between two discrete levels from…
We study a stochastic model of biosynthesis of proteins in generic bacterial operons. The stochasticity arises from two different processes, namely from `bursting' production of either mRNA and/or protein (in the transcription/translation…
Boundary-catalytic branching processes describe a broad class of natural phenomena where the population of diffusing particles grows due to their spontaneous binary branching (e.g., division, fission or splitting) on a catalytic boundary…
Transcriptional pulsing has been observed in both prokaryotes and eukaryotes and plays a crucial role in cell to cell variability of protein and mRNA numbers. The issue is how the time constants associated with episodes of transcriptional…
A self-organized branching process is introduced to describe one-dimensional ricepile model with stochastic topplings. Although the branching processes are generally supposed to describe well the systems in high dimension, our modification…
Stochastic models of surface growth are usually based on randomly choosing a substrate site to perform iterative steps, as in the etching model [1]. In this paper I modify the etching model to perform sequential, instead of random,…
Cell sorting, whereby a heterogeneous cell mixture segregates and forms distinct homogeneous tissues, is one of the main collective cell behaviors at work during development. Although differences in interfacial energies are recognized to be…
Disentangled representation learning (DRL) aims to break down observed data into core intrinsic factors for a profound understanding of the data. In real-world scenarios, manually defining and labeling these factors are non-trivial, making…
We take an image science perspective on the problem of determining brain network connectivity given functional activity. But adapting the concept of image resolution to this problem, we provide a new perspective on network partitioning for…
Classical transition state theory (TST) is the cornerstone of reaction rate theory. It postulates a partition of phase space into reactant and product regions, which are separated by a dividing surface that reactive trajectories must cross.…
Interactions between neighboring cells are essential for generating or refining patterns in a number of biological systems. We propose a discrete filtering approach to predict how networks of cells modulate spatially varying input signals…
Systemic properties of living cells are the result of molecular dynamics governed by so-called genetic regulatory networks (GRN). These networks capture all possible features of cells and are responsible for the immense levels of adaptation…
In conventional cellular networks, for base stations (BSs) that are deployed far away from each other, it is general to assume them to be mutually independent. Nevertheless, after long-term evolution of cellular networks in various…
The clustering of B cell receptor (BCR) molecules and the formation of the protein segregation structure known as the immunological synapse appears to precede antigen (Ag) uptake by B cells. The mature B cell synapse is characterized by a…