Markovian dynamics on complex reaction networks
J Goutsias, G Jenkinson - Physics reports, 2013 - Elsevier
Complex networks, comprised of individual elements that interact with each other through
reaction channels, are ubiquitous across many scientific and engineering disciplines …
reaction channels, are ubiquitous across many scientific and engineering disciplines …
Cooperativity in cellular biochemical processes: noise-enhanced sensitivity, fluctuating enzyme, bistability with nonlinear feedback, and other mechanisms for …
H Qian - Annual review of biophysics, 2012 - annualreviews.org
Cooperativity in classical biophysics originates from molecular interactions; nonlinear
feedbacks in biochemical networks regulate dynamics inside cells. Using stochastic reaction …
feedbacks in biochemical networks regulate dynamics inside cells. Using stochastic reaction …
[HTML][HTML] Architecture-dependent noise discriminates functionally analogous differentiation circuits
Gene regulatory circuits with different architectures (patterns of regulatory interactions) can
generate similar dynamics. This raises the question of why a particular circuit architecture is …
generate similar dynamics. This raises the question of why a particular circuit architecture is …
Stabilizing effect of volatility in financial markets
D Valenti, G Fazio, B Spagnolo - Physical Review E, 2018 - APS
In financial markets, greater volatility is usually considered to be synonymous with greater
risk and instability. However, large market downturns and upturns are often preceded by …
risk and instability. However, large market downturns and upturns are often preceded by …
[HTML][HTML] Computing with biological switches and clocks
The complex dynamics of biological systems is primarily driven by molecular interactions
that underpin the regulatory networks of cells. These networks typically contain positive and …
that underpin the regulatory networks of cells. These networks typically contain positive and …
Mixed-mode oscillations and interspike interval statistics in the stochastic FitzHugh–Nagumo model
N Berglund, D Landon - Nonlinearity, 2012 - iopscience.iop.org
We study the stochastic FitzHugh–Nagumo equations, modelling the dynamics of neuronal
action potentials in parameter regimes characterized by mixed-mode oscillations. The …
action potentials in parameter regimes characterized by mixed-mode oscillations. The …
Biological role of noise encoded in a genetic network motif
M Kittisopikul, GM Süel - Proceedings of the National …, 2010 - National Acad Sciences
Genetic circuits that regulate distinct cellular processes can differ in their wiring pattern of
interactions (architecture) and susceptibility to stochastic fluctuations (noise). Whether the …
interactions (architecture) and susceptibility to stochastic fluctuations (noise). Whether the …
[HTML][HTML] Transitions in a genetic transcriptional regulatory system under Lévy motion
Based on a stochastic differential equation model for a single genetic regulatory system, we
examine the dynamical effects of noisy fluctuations, arising in the synthesis reaction, on the …
examine the dynamical effects of noisy fluctuations, arising in the synthesis reaction, on the …
A statistical approach reveals designs for the most robust stochastic gene oscillators
ML Woods, M Leon, R Perez-Carrasco… - ACS synthetic …, 2016 - ACS Publications
The engineering of transcriptional networks presents many challenges due to the inherent
uncertainty in the system structure, changing cellular context, and stochasticity in the …
uncertainty in the system structure, changing cellular context, and stochasticity in the …
Demethylation and re-expression of epigenetically silenced tumor suppressor genes: sensitization of cancer cells by combination therapy
S Sarkar, S Goldgar, S Byler, S Rosenthal… - …, 2013 - Taylor & Francis
Epigenetic regulation in eukaryotic and mammalian systems is a complex and emerging
field of study. While histone modifications create an open chromatin conformation allowing …
field of study. While histone modifications create an open chromatin conformation allowing …