Related papers: An All-Encompassing Global Convergence Result for …

Phosphorelays are a class of signaling mechanisms used by cells to respond to changes in their environment. Phosphorelays (of which two-component systems constitute a special case) are particularly abundant in prokaryotes and have been…

This work addresses whether a reaction network, taken with mass-action kinetics, is multistationary, that is, admits more than one positive steady state in some stoichiometric compatibility class. We build on previous work on the effect…

Double phosphorylation of protein kinases is a common feature of signalling cascades. This motif may reduce cross-talk between signalling pathways, as the second phosphorylation site allows for proofreading, especially when phosphorylation…

We show that finite-size, disordered molecular networks can mediate highly efficient, coherent excitation transfer which is robust against ambient dephasing and associated with strong multi-site entanglement. Such optimal, random molecular…

Protein phosphorylation is a reversible post-translational modification commonly used by cell signaling networks to transmit information about the extracellular environment into intracellular organelles for the regulation of the activity…

Some of the most common mathematical models in biology, chemistry, physics, and engineering, are polynomial dynamical systems, i.e., systems of differential equations with polynomial right-hand sides. Inspired by notions and results that…

The distributive sequential n-site phosphorylation/dephosphorylation system is an important building block in networks of chemical reactions arising in molecular biology, which has been intensively studied. In the nice paper of Wang and…

Multisite phosphorylation plays an important role in regulating switchlike protein activity and has been used widely in mathematical models. With the development of new experimental techniques and more molecular data, molecular…

The multiple futile cycle is a phosphorylation system in which a molecular substrate might be phosphorylated sequentially n times by means of an enzymatic mechanism. The system has been studied mathematically using reaction network theory…

Molecular systems containing donor-bridge-acceptor sites or molecular antennas constitute promising candidates for organic photovoltaic device implementation. Photo-induced electron transfer in multi-chromophore molecular systems is defined…

The practical description of disordered chemical reactions, where reactions involve multiple species at multiple sites, is presently challenge using correlated electronic structure methods. Here we describe the gradient theory of…

The theory of monotone dynamical systems has been found very useful in the modeling of some gene, protein, and signaling networks. In monotone systems, every net feedback loop is positive. On the other hand, negative feedback loops are…

Here we focus on the challenge of verifying the correctness of molecular implementations of abstract chemical reaction networks, where operation in a well-mixed "soup" of molecules is stochastic, asynchronous, concurrent, and often involves…

We prove that every partial action of an inverse semigroupoid on a set admits a universal globalization. Moreover, we show that our construction gives a reflector from the category of partial actions on the full subcategory of global…

We extend the concept that life is an informational phenomenon, at every level of organisation, from molecules to the global ecological system. According to this thesis: (a) living is information processing, in which memory is maintained by…

The global existence of renormalised solutions and convergence to equilibrium for reaction-diffusion systems with non-linear diffusion are investigated. The system is assumed to have quasi-positive non-linearities and to satisfy an entropy…

When an electron or a hole is added into an orbital of an adsorbed molecule the substrate electrons will rearrange in order to screen the added charge. This results in a reduction of the electron addition/removal energies as compared to the…

Complex networks are a successful framework to describe collective behaviour in many applications, but a notable gap remains in the current literature, that of proving asymptotic convergence in networks of piecewise-smooth systems. Indeed,…

A monolithic process is a single recursive equation with data parameters, which only uses non-determinism, action prefixing, and recursion. We present a technique that decomposes such a monolithic process into multiple processes where each…

Multistationarity in molecular systems underlies switch-like responses in cellular decision making. Determining whether and when a system displays multistationarity is in general a difficult problem. In this work we completely determine the…