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In living cells, chemical reactions are connected by sharing their products and substrates, and form complex networks, e.g. metabolic pathways. Here we developed a theory to predict the sensitivity, i.e. the responses of concentrations and…
Proposals for molecular communication networks as part of a future internet of bio-nano-things have become more intricate and the question of practical implementation is gaining more importance. One option is to apply detailed chemical…
Chemical reaction networks (CRN) comprise an important class of models to understand biological functions such as cellular information processing, the robustness and control of metabolic pathways, circadian rhythms, and many more. However,…
Stochastic evolution of Chemical Reactions Networks (CRNs) over time is usually analysed through solving the Chemical Master Equation (CME) or performing extensive simulations. Analysing stochasticity is often needed, particularly when some…
According to the chemical reaction network theory, the topology of a certain class of chemical reaction networks, regardless of the kinetic details, sets a limit on the dynamical properties that a particular network can potentially admit;…
This paper is a reflexion on the computability of natural language semantics. It does not contain a new model or new results in the formal semantics of natural language: it is rather a computational analysis of the logical models and…
Chemical language models (CLMs) are increasingly used for molecular design and property prediction. Because these models learn from textual encodings of molecules, differences in how such encodings are generated may affect their behavior.…
This paper focuses on molecular communication (MC) systems using two types of signaling molecules which may participate in a reversible bimolecular reaction in the channel. The motivation for studying these MC systems is that they can…
Synthetic active colloidal systems are being studied extensively because of the diverse and often unusual phenomena these nonequilibrium systems manifest, and their potential applications in fields ranging from biology to material science.…
An algorithm is given in this paper for the computation of dynamically equivalent weakly reversible realizations with the maximal number of reactions, for chemical reaction networks (CRNs) with mass action kinetics. The original problem…
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…
Network models are widely used as structural summaries of biochemical systems. Statistical estimation of networks is usually based on linear or discrete models. However, the dynamics of these systems are generally nonlinear, suggesting that…
We study biochemical reaction networks capable of product discrimination inspired by biological proofreading mechanisms. At equilibrium, product discrimination, the selective formation of a "correct" product with respect to an "incorrect…
For several decades, chemical knowledge has been published in written text, and there have been many attempts to make it accessible, for example, by transforming such natural language text to a structured format. Although the discovered…
Molecular processes of neuronal learning have been well-described. However, learning mechanisms of non-neuronal cells have not been fully understood at the molecular level. Here, we discuss molecular mechanisms of cellular learning,…
Generative mechanisms which lead to empirically observed structure of networked systems from diverse fields like biology, technology and social sciences form a very important part of study of complex networks. The structure of many…
Recent research in molecular discovery has primarily been devoted to small, drug-like molecules, leaving many similarly important applications in material design without adequate technology. These applications often rely on more complex…
Systems biology uses large networks of biochemical reactions to model the functioning of biological cells from the molecular to the cellular scale. The dynamics of dissipative reaction networks with many well separated time scales can be…
Chemical reaction networks (CRNs) are prototypical complex systems because reactions are nonlinear and connected in intricate ways, and they are also essential to understand living systems. Here, I discuss how recent developments in…
We discuss the symbolic dynamics of biochemical networks with separate timescales. We show that symbolic dynamics of monomolecular reaction networks with separated rate constants can be described by deterministic, acyclic automata with a…