Universality of phenotypic distributions in bacteria

K Biswas, N Brenner - Physical Review Research, 2024 - APS
Some phenotypic properties in bacteria exhibit universal statistics, with distributions
collapsing under scaling. The extent and origins of such universality are not well …

Characterizing non-exponential growth and bimodal cell size distributions in fission yeast: An analytical approach

C Jia, A Singh, R Grima - PLOS Computational Biology, 2022 - journals.plos.org
Unlike many single-celled organisms, the growth of fission yeast cells within a cell cycle is
not exponential. It is rather characterized by three distinct phases (elongation, septation, and …

Continuous rate modeling of bacterial stochastic size dynamics

C Nieto, C Vargas-Garcia, JM Pedraza - Physical Review E, 2021 - APS
Bacterial division is an inherently stochastic process with effects on fluctuations of protein
concentration and phenotype variability. Current modeling tools for the stochastic short-term …

Stochastic threshold in cell size control

L Luo, Y Bai, X Fu - Physical Review Research, 2023 - APS
Classic models of cell size control consider that cells divide when reaching a threshold, eg,
size, age, or size extension. The molecular basis of the threshold involves multiple layers of …

Pyecolib: a python library for simulating stochastic cell size dynamics

C Nieto, SC Blanco, C Vargas-García, A Singh… - Physical …, 2023 - iopscience.iop.org
Recently, there has been an increasing need for tools to simulate cell size regulation due to
important applications in cell proliferation and gene expression. However, implementing the …

Joint distribution of protein concentration and cell volume coupled by feedback in dilution

I Zabaikina, P Bokes, A Singh - International Conference on Computational …, 2023 - Springer
We consider a protein that negatively regulates the rate with which a cell grows. Since less
growth means less protein dilution, this mechanism forms a positive feedback loop on the …

Concentration fluctuations due to size-dependent gene expression and cell-size control mechanisms

C Jia, A Singh, R Grima - BioRxiv, 2021 - biorxiv.org
Intracellular reaction rates depend on concentrations and hence their levels are often
regulated. However classical models of stochastic gene expression lack a cell size …

Cell size control shapes fluctuations in colony population

C Nieto, C Vargas-García, JM Pedraza… - 2022 IEEE 61st …, 2022 - ieeexplore.ieee.org
Exponentially growing cells regulate their size by controlling their timing of division. Since
two daughter cells are born as a result of this cell splitting, cell size regulation has a direct …

Large deviations and fluctuation theorems for cycle currents defined in the loop-erased and spanning tree manners: a comparative study

Y Jiang, B Wu, C Jia - Physical Review Research, 2023 - APS
The cycle current is a crucial quantity in stochastic thermodynamics. The absolute and net
cycle currents of a Markovian system can be defined in the loop-erased (LE) or spanning …

Branching processes with resetting as a model for cell division

A Genthon, R García-García… - Journal of Physics A …, 2022 - iopscience.iop.org
We study the stochastic thermodynamics of cell growth and division using a theoretical
framework based on branching processes with resetting. Cell division may be split into two …