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Gene transcription is a highly stochastic and dynamic process. As a result, the mRNA copy number of a given gene is heterogeneous both between cells and across time. We present a framework to model gene transcription in populations of cells…
We introduce and study a class of optimization problems we coin replenishment problems with fixed turnover times: a very natural model that has received little attention in the literature. Nodes with capacity for storing a certain commodity…
The effects of stochastic apppearence of embryos of a new phase are analyzed analytically. A new approach by the similarity of nucleation conditions is proposed. Corrections for a number of droplets are estimated. A comparison with…
Turnover of regulatory sequence and function is an important part of molecular evolution. But what are the modes of sequence evolution leading to rapid formation and loss of regulatory sites? Here, we show that a large fraction of…
DNA polymerase (DNAP) is a dual-purpose enzyme that plays two opposite roles in two different situations during DNA replication. It plays its normal role as a {\it polymerase} catalyzing the elongation of a new DNA molecule by adding a…
Biological systems perform complex multi-step processes in a reproducible way despite underlying stochasticity. The standard explanation is micromanagement by molecular machinery that recognizes and corrects specific errors. Here we study…
Reservoir Computing (RC), a type of recurrent random neural network, is a powerful framework for modeling complex and chaotic dynamics. However, its autonomous (closed-loop) operation is often plagued by inherent instability. Moreover,…
Expression of many genes varies as a cell transitions through different cell-cycle stages. How coupling between stochastic expression and cell cycle impacts cell-to-cell variability (noise) in the level of protein is not well understood. We…
Replicating systems sustained by error-prone enzymatic amplification can undergo critical transitions between persistence and extinction. In RNA viruses, such transitions are classically governed by mutation rates and fitness landscapes,…
A correlation between karyotype diversity and species richness was first observed in mammals in 1980, and subsequently confirmed after controlling for phylogenetic signal. The correlation was attributed to submicroscopic factors, presumably…
In order to survive, reproduce and (in multicellular organisms) differentiate, cells must control the concentrations of the myriad different proteins that are encoded in the genome. The precision of this control is limited by the inevitable…
Quasispecies theory provides the conceptual and theoretical bases for describing the dynamics of biological information of replicators subject to large mutation rates. This theory, initially conceived within the framework of prebiotic…
In biological cells, DNA replication is carried out by the replisome, a protein complex encompassing multiple DNA polymerases. DNA replication is semi-discontinuous: a DNA polymerase synthesizes one (leading) strand of the DNA continuously,…
We study the optimal sequencing of a batch of tasks on a machine subject to random disruptions driven by a non-homogeneous Poisson process (NHPP), such that every disruption requires the interrupted task to be re-processed from scratch, and…
Multiple phenotypic states often arise in a single cell with different gene-expression states that undergo transcription regulation with positive feedback. Recent experiments have shown that at least in E. coli, the gene state switching can…
DNA synthesis is considered as one of the most expensive components in current DNA storage systems. In this paper, focusing on a common synthesis machine, which generates multiple DNA strands in parallel following a fixed supersequence,we…
Delay is an important and ubiquitous aspect of many biochemical processes. For example, delay plays a central role in the dynamics of genetic regulatory networks as it stems from the sequential assembly of first mRNA and then protein.…
The reliance of organisations on computer networks is enabled by network programmability, which is typically achieved through Service Function Chaining. These chains virtualise network functions, link them, and programmatically embed them…
We present a method for enhanced sampling of molecular dynamics simulations using stochastic resetting. Various phenomena, ranging from crystal nucleation to protein folding, occur on timescales that are unreachable in standard simulations.…
This paper studies two problems that are motivated by the novel recent approach of composite DNA that takes advantage of the DNA synthesis property which generates a huge number of copies for every synthesized strand. Under this paradigm,…