Biochemical reaction networks often display robust responses to persistent perturbations despite high dimensionality, feedback, and uncertain kinetics. Classical robust perfect adaptation (RPA) captures one important mechanism: after sustained input changes, a designated output returns to a fixed steady state independent of perturbation magnitude. However, many cellular systems do not relax to...
In living cells, numerous chemical reactions are interconnected by sharing substrates and products, forming a reaction network. Various functions of cells emerge from dynamics of such interconnected system. Cells regulate amount of key chemicals by controlling amount/activity of enzymes, thereby achieving control of cellular functions. However, in such an interconnected system, can different...
In this talk I will share recent results on how to detect whether a reaction network with mass-action kinetics admits a monomial parametrization or displays absolute concentration robustness. When requiring that either property arises in an open subset of parameter space, both problems can be approached by an initial check using linear algebra, and a second check where a more detailed analysis...
Cycling reaction networks are ubiquitous in nature,
underpinning key processes such as the Krebs and Kelvin
cycles. In this talk, we analyze the robustness of such networks.
Under the regularity assumptionโthat all supplied species are
subject to degradationโwe show that the dynamics converge to
a consensus state, where all external and internal flows equalize
while species...
Fundamental properties and emergent behaviours of biochemical systems often depend exclusively on the system structure (the graph topology along with qualitative information), regardless of parameter values. We first provide an overview of the parameter-free assessment of important properties, including the stability of equilibria and the sign of steady-state input-output influences. Then, we...
In recent years, there have been a few uses of the word โcoreโ in the context of chemical reaction networks, all related to some idea of minimality. Based on stoichiometric considerations alone (i.e. no dynamics nor kinetic considerations involved), Alex Blokhuis with co-authors identified autocatalytic cores as minimal structures carrying autocatalysis, a fundamental biochemical concept...
A response curve measures the output of a biological system at equilibrium against an input parameter $u$, which could be a rate constant, or amount of a stimulus (poison, drug, ligand, etc.). Of interest is the shape of a response curve: does it have a plateau region (homeostasis); is it monotonic? In T-cell's response to antigen, a non-monotonic (i.e., biphasic) response has been observed....
Cellular phenotypes exhibit remarkable diversity, reflecting the complex functional states of individual cells. Although phenotypic diversity has traditionally been assessed at the transcriptomic level, recent advances in single-cell technologies have shifted attention toward metabolomic phenotyping, which provides a more direct reflection of cellular function. Nonetheless, the high...
Biological functions emerge from the dynamics of complex chemical reaction networks comprising of multiple interacting biomolecules within cells. Understanding the dynamics of such chemical reaction systems is therefore central to elucidating biological function. However, the inherent complexity of these systems has made rigorous analytical characterisation of their dynamical behaviour...
