WKB theory of large deviations in stochastic populations
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 …
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 …
necessarily occur in single steps of individual molecules, and, conversely, each birth or …
Dynamics of simple gene-network motifs subject to extrinsic fluctuations
Cellular processes do not follow deterministic rules; even in identical environments
genetically identical cells can make random choices leading to different phenotypes. This …
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 …
payoff a strategy receives. The payoff depends on the environment that may change over …
Escape from a metastable state in non-Markovian population dynamics
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 …
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
The paper outlines a general approach to deriving quasi-steady-state approximations
(QSSAs) of the stochastic reaction networks describing the Michaelis–Menten enzyme …
(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
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 …
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 …
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
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 …
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 …
or the concentrations of reactive species, making molecular approaches necessary for …