WKB theory of large deviations in stochastic populations

M Assaf, B Meerson - Journal of Physics A: Mathematical and …, 2017 - iopscience.iop.org
Stochasticity can play an important role in the dynamics of biologically relevant populations.
These span a broad range of scales: from intra-cellular populations of molecules to …

Markovian approaches to modeling intracellular reaction processes with molecular memory

J Zhang, T Zhou - Proceedings of the National Academy of …, 2019 - National Acad Sciences
Many cellular processes are governed by stochastic reaction events. These events do not
necessarily occur in single steps of individual molecules, and, conversely, each birth or …

Dynamics of simple gene-network motifs subject to extrinsic fluctuations

E Roberts, S Be'er, C Bohrer, R Sharma, M Assaf - Physical Review E, 2015 - APS
Cellular processes do not follow deterministic rules; even in identical environments
genetically identical cells can make random choices leading to different phenotypes. This …

Unfair and anomalous evolutionary dynamics from fluctuating payoffs

F Stollmeier, J Nagler - Physical review letters, 2018 - APS
Evolution occurs in populations of reproducing individuals. Reproduction depends on the
payoff a strategy receives. The payoff depends on the environment that may change over …

Escape from a metastable state in non-Markovian population dynamics

O Vilk, M Assaf - Physical Review E, 2024 - APS
We study the long-time dynamics in non-Markovian single-population stochastic models,
where one or more reactions are modeled as a stochastic process with a fat-tailed …

Quasi-steady-state approximations derived from the stochastic model of enzyme kinetics

HW Kang, WR KhudaBukhsh, H Koeppl… - Bulletin of mathematical …, 2019 - Springer
The paper outlines a general approach to deriving quasi-steady-state approximations
(QSSAs) of the stochastic reaction networks describing the Michaelis–Menten enzyme …

A computational method for the investigation of multistable systems and its application to genetic switches

M Leon, ML Woods, AJH Fedorec, CP Barnes - BMC systems biology, 2016 - Springer
Background Genetic switches exhibit multistability, form the basis of epigenetic memory, and
are found in natural decision making systems, such as cell fate determination in …

The distributed delay rearranges the bimodal distribution at protein level

LJ Chiu, MY Ling, EH Wu, CX You, ST Lin… - Journal of the Taiwan …, 2022 - Elsevier
Background In bimodal distribution, we refer ON to the mode with a higher protein level and
OFF to a lower protein level. The traditional wisdom of manipulating the population in each …

High cooperativity in negative feedback can amplify noisy gene expression

P Bokes, YT Lin, A Singh - Bulletin of Mathematical Biology, 2018 - Springer
Burst-like synthesis of protein is a significant source of cell-to-cell variability in protein levels.
Negative feedback is a common example of a regulatory mechanism by which such …

Generalized fluctuation-dissipation theorem for non-Markovian reaction networks

A Chen, H Qiu, T Tian, T Zhou - Physical Review E, 2022 - APS
Intracellular biochemical networks often display large fluctuations in the molecule numbers
or the concentrations of reactive species, making molecular approaches necessary for …