Taking chances and making mistakes: non-genetic phenotypic heterogeneity and its consequences for surviving in dynamic environments

C van Boxtel, JH van Heerden… - Journal of The …, 2017 - royalsocietypublishing.org
Natural selection has shaped the strategies for survival and growth of microorganisms. The
success of microorganisms depends not only on slow evolutionary tuning but also on the …

Dynamic fluctuations in a bacterial metabolic network

S Bi, M Kargeti, R Colin, N Farke, H Link… - Nature …, 2023 - nature.com
The operation of the central metabolism is typically assumed to be deterministic, but
dynamics and high connectivity of the metabolic network make it potentially prone to …

Framing climate uncertainty: socio-economic and climate scenarios in vulnerability and adaptation assessments

F Berkhout, B van den Hurk, J Bessembinder… - Regional environmental …, 2014 - Springer
Scenarios have become a powerful tool in integrated assessment and policy analysis for
climate change. Socio-economic and climate scenarios are often combined to assess …

How molecular competition influences fluxes in gene expression networks

D De Vos, FJ Bruggeman, HV Westerhoff, BM Bakker - PloS one, 2011 - journals.plos.org
Often, in living cells different molecular species compete for binding to the same molecular
target. Typical examples are the competition of genes for the transcription machinery or the …

Nonlinear signalling networks and cell-to-cell variability transform external signals into broadly distributed or bimodal responses

M Dobrzyński, LK Nguyen… - Journal of The …, 2014 - royalsocietypublishing.org
We show theoretically and experimentally a mechanism behind the emergence of wide or
bimodal protein distributions in biochemical networks with nonlinear input–output …

Optimality principles in the regulation of metabolic networks

J Berkhout, FJ Bruggeman, B Teusink - Metabolites, 2012 - mdpi.com
One of the challenging tasks in systems biology is to understand how molecular networks
give rise to emergent functionality and whether universal design principles apply to …

Single yeast cells vary in transcription activity not in delay time after a metabolic shift

A Schwabe, FJ Bruggeman - Nature communications, 2014 - nature.com
Individual cells respond very differently to changes in environmental conditions.
Stochasticity causes cells to respond at different times, magnitudes or both. Here we …

A large deviations principle for infinite-server queues in a random environment

HM Jansen, MRH Mandjes, K De Turck… - Queueing Systems, 2016 - Springer
This paper studies an infinite-server queue in a random environment, meaning that the
arrival rate, the service requirements, and the server work rate are modulated by a general …

Discretised Flux Balance Analysis for Reaction–Diffusion Simulation of Single-Cell Metabolism

YH Chew, F Spill - Bulletin of Mathematical Biology, 2024 - Springer
Metabolites have to diffuse within the sub-cellular compartments they occupy to specific
locations where enzymes are, so reactions could occur. Conventional flux balance analysis …

Impact of the cell division cycle on gene circuits

V Bierbaum, S Klumpp - Physical biology, 2015 - iopscience.iop.org
In growing cells, protein synthesis and cell growth are typically not synchronous, and, thus,
protein concentrations vary over the cell division cycle. We have developed a theoretical …