Noise in biology

LS Tsimring - Reports on Progress in Physics, 2014 - iopscience.iop.org
Noise permeates biology on all levels, from the most basic molecular, sub-cellular
processes to the dynamics of tissues, organs, organisms and populations. The functional …

Bistability, epigenetics, and bet-hedging in bacteria

JW Veening, WK Smits, OP Kuipers - Annu. Rev. Microbiol., 2008 - annualreviews.org
Clonal populations of microbial cells often show a high degree of phenotypic variability
under homogeneous conditions. Stochastic fluctuations in the cellular components that …

A stochastic single-molecule event triggers phenotype switching of a bacterial cell

PJ Choi, L Cai, K Frieda, XS Xie - Science, 2008 - science.org
By monitoring fluorescently labeled lactose permease with single-molecule sensitivity, we
investigated the molecular mechanism of how an Escherichia coli cell with the lac operon …

Markovian dynamics on complex reaction networks

J Goutsias, G Jenkinson - Physics reports, 2013 - Elsevier
Complex networks, comprised of individual elements that interact with each other through
reaction channels, are ubiquitous across many scientific and engineering disciplines …

Phenotypic model for early T-cell activation displaying sensitivity, specificity, and antagonism

P François, G Voisinne, ED Siggia… - Proceedings of the …, 2013 - National Acad Sciences
Early T-cell activation is selected by evolution to discriminate a few foreign peptides rapidly
from a vast excess of self-peptides, and it is unclear in quantitative terms how this is …

Noise-induced mechanism for biological homochirality of early life self-replicators

F Jafarpour, T Biancalani, N Goldenfeld - Physical review letters, 2015 - APS
The observed single-handedness of biological amino acids and sugars has long been
attributed to autocatalysis. However, the stability of homochiral states in deterministic …

Nonequilibrium thermodynamics in cell biology: Extending equilibrium formalism to cover living systems

X Fang, J Wang - Annual review of biophysics, 2020 - annualreviews.org
We discuss new developments in the nonequilibrium dynamics and thermodynamics of
living systems, giving a few examples to demonstrate the importance of nonequilibrium …

A comparison of deterministic and stochastic modeling approaches for biochemical reaction systems: On fixed points, means, and modes

SK Hahl, A Kremling - Frontiers in genetics, 2016 - frontiersin.org
In the mathematical modeling of biochemical reactions, a convenient standard approach is
to use ordinary differential equations (ODEs) that follow the law of mass action. However …

Cooperativity in cellular biochemical processes: noise-enhanced sensitivity, fluctuating enzyme, bistability with nonlinear feedback, and other mechanisms for …

H Qian - Annual review of biophysics, 2012 - annualreviews.org
Cooperativity in classical biophysics originates from molecular interactions; nonlinear
feedbacks in biochemical networks regulate dynamics inside cells. Using stochastic reaction …

Stochastic phenotype transition of a single cell in an intermediate region of gene state switching

H Ge, H Qian, XS Xie - Physical review letters, 2015 - APS
Multiple phenotypic states often arise in a single cell with different gene-expression states
that undergo transcription regulation with positive feedback. Recent experiments show that …