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Zero-one biochemical reaction networks play key roles in cell signalling such as signalling pathways regulated by protein phosphorylation. Multistability of reaction networks is a crucial dynamics feature enabling decision-making in cells.…
We address several questions in reduced versus extended networks via the elimination or addition of intermediate complexes in the framework of chemical reaction networks with mass-action kinetics. We clarify and extend advances in the…
A numerical algorithm to obtain the consistent conditions satisfied by singular arcs for singular linear-quadratic optimal control problems is presented. The algorithm is based on the presymplectic constraint algorithm (PCA) by Gotay-Nester…
High-multiplicity signatures at particle colliders can arise in Standard Model processes and beyond. With such signatures, difficulties often arise from the large dimensionality of the kinematic space. For final states containing a single…
The well-known Deficiency One Theorem gives structural conditions on a chemical reaction network under which, for any set of parameter values, the steady states of the corresponding mass action system may be easily characterized. It is also…
We answer several fundamental geometric questions about reaction networks with power-law kinetics, on topics such as generic finiteness of the number of steady states, robustness, and nondegenerate multistationarity. In particular, we give…
This paper analyzes stochastic networks consisting of a set of finite capacity sites where different classes of individuals move according to some routing policy. The associated Markov jump processes are analyzed under a thermodynamic limit…
Controllability and observability energy functions play a fundamental role in model order reduction and are inherently connected to optimal control problems. For linear dynamical systems the energy functions are known to be quadratic…
We use ideas from kinetic proofreading, an error-correcting mechanism in biology, to identify new kinetic regimes in non-equilibrium systems. These regimes are defined by the sensitivity of the occupancy of a state of the system to a change…
Under mass-action kinetics, biochemical reaction networks give rise to polynomial autonomous dynamical systems whose parameters are often difficult to estimate. We deal in this paper with the problem of identifying the kinetic parameters of…
Stochastic modeling of reaction networks is a framework used to describe the time evolution of many natural and artificial systems, including, biochemical reactive systems at the molecular level, viral kinetics, the spread of epidemic…
We investigate models of the mitogenactivated protein kinases (MAPK) network, with the aim of determining where in parameter space there exist multiple positive steady states. We build on recent progress which combines various symbolic…
In the past few decades, the development of fluorescent technologies and microscopic techniques has greatly improved scientists' ability to observe real-time single-cell activities. In this paper, we consider the filtering problem associate…
A multistable system generated by a Piecewise Linear (PWL) system based on the jerky equation is presented. The systems behaviour is characterised by means of the Nearest Integer or round(x) function to control the switching events and to…
Power grid operation is becoming more complex due to the increase in generation of renewable energy. The recent series of Learning To Run a Power Network (L2RPN) competitions have encouraged the use of artificial agents to assist human…
Controlling complex reaction networks is a fundamental challenge in the fields of physics, biology, and systems engineering. Here, we prove a general principle for catalytic reaction systems with kinetics where the reaction order and the…
Mass-action kinetics is frequently used in systems biology to model the behaviour of interacting chemical species. Many important dynamical properties are known to hold for such systems if they are weakly reversible and have a low…
This paper presents new results about the optimization based generation of chemical reaction networks (CRNs) of higher deficiency. Firstly, it is shown that the graph structure of the realization containing the maximal number of reactions…
The stochastic description of chemical reaction networks with the kinetic chemical master equation (CME) is important for studying biological cells, but it suffers from the curse of dimensionality: The amount of data to be stored grows…
We consider the problem of efficiently performing simulation and inference for stochastic kinetic models. Whilst it is possible to work directly with the resulting Markov jump process, computational cost can be prohibitive for networks of…