A stochastic vs deterministic perspective on the timing of cellular events

L Ham, MA Coomer, K Öcal, R Grima… - Nature …, 2024 - nature.com
Cells are the fundamental units of life, and like all life forms, they change over time. Changes
in cell state are driven by molecular processes; of these many are initiated when molecule …

Exact distribution of threshold crossing times for protein concentrations: Implication for biological timekee**

K Rijal, A Prasad, A Singh, D Das - Physical Review Letters, 2022 - APS
Stochastic protein accumulation up to some concentration threshold sets the timing of many
cellular physiological processes. Here we obtain the exact distribution of first threshold …

Controlling gene expression timing through gene regulatory architecture

MZ Ali, RC Brewster - PLoS Computational Biology, 2022 - journals.plos.org
Gene networks typically involve the regulatory control of multiple genes with related function.
This connectivity enables correlated control of the levels and timing of gene expression …

First passage time in post-transcriptional regulation by multiple small RNAs

K Biswas, A Ghosh - The European Physical Journal E, 2021 - Springer
The post-transcriptional regulation of a protein by multiple small RNA molecules has been
formulated as a stochastic process. An approximate solution of the master equation shows …

First passage time properties of miRNA-mediated protein translation

K Biswas, MK Jolly, A Ghosh - Journal of Theoretical Biology, 2021 - Elsevier
An important function of microRNAs in gene regulation is to repress the protein synthesis in
a multi-step process with implications in timing efficiency of the regulatory network. We …

Timing effciency in small-rna-regulated post-transcriptional processes

K Biswas, A Ghosh - Physical Review E, 2020 - APS
Gene regulation in a cellular environment is a stochastic phenomenon leading to a large
variability in mRNAs and protein numbers that are often produced in bursts. The regulation …

Feedback strategies for threshold crossing of protein levels at a prescribed time

C Nieto, KR Ghusinga, A Singh - 2022 30th Mediterranean …, 2022 - ieeexplore.ieee.org
The timing of diverse cellular processes is based on the instant when the concentration of
regulatory proteins crosses a critical threshold level. Hence, noise mechanisms inherent to …

Effect of gene-expression bursts on stochastic timing of cellular events

KR Ghusinga, A Singh - 2017 American Control Conference …, 2017 - ieeexplore.ieee.org
Gene expression is inherently a noisy process which manifests as cell-to-cell variability in
time evolution of proteins. Consequently, events that trigger at critical threshold levels of …

Spatial moment description of birth–death–movement processes incorporating the effects of crowding and obstacles

A Surendran, MJ Plank, MJ Simpson - Bulletin of Mathematical Biology, 2018 - Springer
Birth–death–movement processes, modulated by interactions between individuals, are
fundamental to many cell biology processes. A key feature of the movement of cells within in …

First-passage time statistics of stochastic transcription process for time-dependent reaction rates

K Biswas, M Shreshtha, A Surendran… - The European Physical …, 2019 - Springer
Transcription in gene expression is an intrinsically noisy process which involves production
and degradation of mRNAs. An important quantity to describe this stochastic process is the …