Theoretical aspects of cellular decision-making and information-processing

TJ Kobayashi, A Kamimura - Advances in Systems Biology, 2012 - Springer
Microscopic biological processes have extraordinary complexity and variety at the sub-
cellular, intra-cellular, and multi-cellular levels. In dealing with such complex phenomena …

Connection between the bacterial chemotactic network and optimal filtering

K Nakamura, TJ Kobayashi - Physical Review Letters, 2021 - APS
The chemotactic network of Escherichia coli has been studied extensively both biophysically
and information theoretically. Nevertheless, connection between these two aspects is still …

Theoretical analysis of discreteness-induced transition in autocatalytic reaction dynamics

N Saito, K Kaneko - Physical Review E, 2015 - APS
Transitions in the qualitative behavior of chemical reaction dynamics with a decrease in
molecule number have attracted much attention. Here, a method based on a Markov …

Speed-dependent cellular decision making in nonequilibrium genetic circuits

NR Nene, J Garca-Ojalvo, A Zaikin - PloS one, 2012 - journals.plos.org
Despite being governed by the principles of nonequilibrium transitions, gene expression
dynamics underlying cell fate decision is poorly understood. In particular, the effect of …

Noise-induced symmetry breaking in a network of excitable ecological systems

A Narang, T Banerjee, PS Dutta - Physical Review E, 2023 - APS
Noise-induced symmetry breaking has barely been unveiled on the ecological grounds,
though its occurrence may elucidate mechanisms responsible for maintaining biodiversity …

Noise-induced bistability in a simple mutual inhibition system

T Haruna, T Shirakawa - Physical Review E, 2023 - APS
In this study, we study noise-induced bistability in a simple bivariate mutual inhibition system
with slow fluctuating responses to external signals. We give a general condition that the …

Constrained Langevin approximation for the Togashi-Kaneko model of autocatalytic reactions

WTL Fan, YJ Yang, C Yuan - arXiv preprint arXiv:2209.00426, 2022 - arxiv.org
The Togashi Kaneko model (TK model), introduced by Togashi and Kaneko in 2001, is a
simple stochastic reaction network that displays discreteness-induced transitions between …

[HTML][HTML] Motif analysis for small-number effects in chemical reaction dynamics

N Saito, Y Sughiyama, K Kaneko - The Journal of chemical physics, 2016 - pubs.aip.org
The number of molecules involved in a cell or subcellular structure is sometimes rather
small. In this situation, ordinary macroscopic-level fluctuations can be overwhelmed by non …

Increased habitat connectivity induces diversity via noise-induced symmetry breaking

A Narang, T Banerjee, P Sharathi Dutta - Chaos: An Interdisciplinary …, 2023 - pubs.aip.org
Stochasticity or noise is omnipresent in ecosystems that mediates community dynamics. The
beneficial role of stochasticity in enhancing species coexistence and, hence, in promoting …

Interplay between path and speed in decision making by high-dimensional stochastic gene regulatory networks

NR Nene, A Zaikin - PLoS One, 2012 - journals.plos.org
Induction of a specific transcriptional program by external signaling inputs is a crucial aspect
of intracellular network functioning. The theoretical concept of coexisting attractors …