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

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 …

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 …

Comparing feedback strategies for minimizing noise in gene expression event timing

Z Vahdat, KR Ghusinga, A Singh - 2021 29th Mediterranean …, 2021 - ieeexplore.ieee.org
Many cellular events occur when their corresponding regulatory proteins attain critical
thresholds. Can cells schedule such events with precision by controlling the dynamics of the …

Universal tradeoff relation between speed, uncertainty, and dissipation in nonequilibrium stationary states

I Neri - SciPost Physics, 2022 - scipost.org
We derive universal thermodynamic inequalities that bound from below the moments of first-
passage times of stochastic currents in nonequilibrium stationary states of Markov jump …

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 …

Mixed-feedback architectures for precise event timing through stochastic accumulation of biomolecules

S Rezaee, C Nieto, A Singh - bioRxiv, 2023 - biorxiv.org
The timing of biochemical events is often determined by the accumulation of a protein or
chemical species to a critical threshold level. In a stochastic model, we define event timing …

Cell-division time statistics from stochastic exponential threshold-crossing

K Biswas, N Brenner - BioRxiv, 2022 - biorxiv.org
For cell division to take place, proteins that carry it out need to accumulate to a functional
threshold. Most of these divisome proteins are highly abundant in the cell, and accumulate …

[PDF][PDF] Dissipation bounds the moments of first-passage times of dissipative currents in nonequilibrium stationary states

I Neri - arXiv preprint arXiv:2103.15007, 2021 - scholar.archive.org
We derive generic thermodynamic bounds on the moments of first-passage times of
dissipative currents in nonequilibrium stationary states. These bounds hold generically for …

Molecular Sequestration Enhances Precision in Timing of Intracellular Events

K Biswas, S Dey, A Singh - bioRxiv, 2024 - biorxiv.org
Expressed gene products often interact ubiquitously with binding sites at nucleic acids and
macromolecular complexes, known as decoys. Binding of transcription factors (TFs) to …

The timing of cellular events: a stochastic vs deterministic perspective

L Ham, MA Coomer, K Öcal, R Grima, MPH Stumpf - bioRxiv, 2023 - biorxiv.org
Changes in cell state are driven by key molecular events whose timing can often be
measured experimentally. Of particular interest is the time taken for the levels of RNA or …