Grip on complexity in chemical reaction networks
A new discipline of “systems chemistry” is emerging, which aims to capture the complexity
observed in natural systems within a synthetic chemical framework. Living systems rely on …
observed in natural systems within a synthetic chemical framework. Living systems rely on …
Network medicine: linking disorders
RM Piro - Human genetics, 2012 - Springer
The molecular events underlying many human hereditary disorders remain to be discovered
despite the significant advances made in molecular biology and genetics in the past years …
despite the significant advances made in molecular biology and genetics in the past years …
Piecewise-linear Lyapunov functions for structural stability of biochemical networks
F Blanchini, G Giordano - Automatica, 2014 - Elsevier
We consider the problem of assessing structural stability of biochemical reaction networks
with monotone reaction rates, namely of establishing if all the networks with a certain …
with monotone reaction rates, namely of establishing if all the networks with a certain …
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 …
Stochastic analysis of biochemical reaction networks with absolute concentration robustness
DF Anderson, GA Enciso… - Journal of The Royal …, 2014 - royalsocietypublishing.org
It has recently been shown that structural conditions on the reaction network, rather than a
'fine-tuning'of system parameters, often suffice to impart 'absolute concentration …
'fine-tuning'of system parameters, often suffice to impart 'absolute concentration …
Vlasov equations on digraph measures
Many science phenomena are described as interacting particle systems (IPS). The mean
field limit (MFL) of large all-to-all coupled deterministic IPS is given by the solution of a PDE …
field limit (MFL) of large all-to-all coupled deterministic IPS is given by the solution of a PDE …
Ultrasensitive molecular controllers for quasi-integral feedback
CC Samaniego, E Franco - Cell Systems, 2021 - cell.com
Feedback control has enabled the success of automated technologies by mitigating the
effects of variability, unknown disturbances, and noise. While it is known that biological …
effects of variability, unknown disturbances, and noise. While it is known that biological …
Computing the structural influence matrix for biological systems
We consider the problem of identifying structural influences of external inputs on steady-
state outputs in a biological network model. We speak of a structural influence if, upon a …
state outputs in a biological network model. We speak of a structural influence if, upon a …
Structural analysis in biology: A control-theoretic approach
F Blanchini, G Giordano - Automatica, 2021 - Elsevier
Despite their complexity, biological systems are able to endure huge parameter fluctuations
and survive in the most diverse environmental conditions. Mathematical tools from graph …
and survive in the most diverse environmental conditions. Mathematical tools from graph …
Polyhedral Lyapunov functions structurally ensure global asymptotic stability of dynamical networks iff the Jacobian is non-singular
F Blanchini, G Giordano - Automatica, 2017 - Elsevier
For a vast class of dynamical networks, including chemical reaction networks (CRNs) with
monotonic reaction rates, the existence of a polyhedral Lyapunov function (PLF) implies …
monotonic reaction rates, the existence of a polyhedral Lyapunov function (PLF) implies …