Related papers: From Electric Circuits to Chemical Networks
The electromagnetic analog of an elastic spring-mass network is constructed. These electromagnetic circuits offer the promise of manipulating electromagnetic fields in new ways, and linear electrical circuits correspond to a subclass of…
Electronic circuits are useful tools for studying potential dynamical behaviors of synthetic genetic networks. The circuit models are complementary to numerical simulations of the networks, especially providing a framework for verification…
Akin to electric circuits, we construct biocircuits that are manipulated by cutting and assembling channels through which stochastic information flows. This diagrammatic manipulation allows us to create a method which constructs networks by…
This paper addresses the decomposition of biochemical networks into functional modules that preserve their dynamic properties upon interconnection with other modules, which permits the inference of network behavior from the properties of…
We lay the foundation of a circuit theory for chemical reaction networks. Chemical reactions are grouped into chemical modules solely characterized by their current-concentration characteristic, as electrical devices by their…
Biochemical networks are used in computational biology, to model the static and dynamical details of systems involved in cell signaling, metabolism, and regulation of gene expression. Parametric and structural uncertainty, as well as…
Bio-inspired neural networks have the potential to advance our understanding of neural computation and improve the state-of-the-art of AI systems. Bio-electrical synapses directly transmit neural signals, by enabling fast current flow…
This paper is concerned with the synthesis of RC electrical circuits from physics-based supercapacitor models describing conservation and diffusion relationships. The proposed synthesis procedure uses model discretisation, linearisation,…
Chemical reactions involve the movement of charges, and this work presents a mathematical model for describing chemical reactions in electrolytes. The model is developed using an energy variational method that aligns with classical…
Molecular circuits capable of autonomous learning could unlock novel applications in fields such as bioengineering and synthetic biology. To this end, existing chemical implementations of neural computing have mainly relied on emulating…
Several abilities of biological systems, such as adaptation to natural environment, or of animals to learn patterns when appropriately trained, are features that are extremely useful, if emulated by electronic circuits, in applications…
We study the dynamic range of a cellular automaton model for a neuronal network with electrical and chemical synapses. The neural network is separated into two layers, where one layer corresponds to inhibitory, and the other corresponds to…
Complex systems such as ecological communities and neuron networks are essential parts of our everyday lives. These systems are composed of units which interact through intricate networks. The ability to predict sudden changes in the…
The analysis of complex reaction networks is of great importance in several chemical and biochemical fields (interstellar chemistry, prebiotic chemistry, reaction mechanism, etc). In this article, we propose to simultaneously refine and…
To unveil the logic of cell from a level of chemical reaction dynamics, we need to clarify how ensemble of chemicals can autonomously produce the set of chemical, without assuming a specific external control echanism. A cell consists of a…
The Bond Graph approach and the Chemical Reaction Network approach to modelling biomolecular systems developed independently. This paper brings together the two approaches by providing a bond graph interpretation of the chemical reaction…
In living cells, chemical reactions form a complex network. Complicated dynamics arising from such networks are the origins of biological functions. We propose a novel mathematical method to analyze bifurcation behaviors of a reaction…
Real-world complex systems such as ecological communities and neuron networks are essential parts of our everyday lives. These systems are composed of units which interact through intricate networks. The ability to predict sudden changes in…
The design and synthesis of complex and large mimicked biochemical networks de novo is an unsolved problem in synthetic biology. To address this limitation without resorting to ad hoc computations and experiments, a predictive mathematical…
Complex network dynamics have been analyzed with models of systems of coupled switches or systems of coupled oscillators. However, many complex systems are composed of components with diverse dynamics whose interactions drive the system's…