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Stochastic reaction networks are a fundamental model to describe interactions between species where random fluctuations are relevant. The master equation provides the evolution of the probability distribution across the discrete state space…
The reaction-diffusion master equation (RDME) is a lattice-based stochastic model for spatially resolved cellular processes. It is often interpreted as an approximation to spatially continuous reaction-diffusion models, which, in the limit…
Diffusion-based molecular communication over nanonetworks is an emerging communication paradigm that enables nanomachines to communicate by using molecules as the information carrier. For such a communication paradigm, Concentration Shift…
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…
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…
Stochastic reaction network models are widely utilized in biology and chemistry to describe the probabilistic dynamics of biochemical systems in general, and gene interaction networks in particular. Most often, statistical analysis and…
The notion of synthetic molecular communication (MC) refers to the transmission of information via molecules and is largely foreseen for use within the human body, where traditional electromagnetic wave (EM)-based communication is…
The mesoscopic reaction-diffusion master equation (RDME) is a popular modeling framework, frequently applied to stochastic reaction-diffusion kinetics in systems biology. The RDME is derived from assumptions about the underlying physical…
Molecular communication in nature can incorporate a large number of nano-things in nanonetworks as well as demonstrate how nano-things communicate. This paper presents molecular communication where transmit nanomachines deliver information…
To model bio-chemical reaction systems with diffusion one can either use stochastic, microscopic reaction-diffusion master equations or deterministic, macroscopic reaction-diffusion system. The connection between these two models is not…
The noisy dynamics of chemical systems is commonly studied using either the chemical master equation (CME) or the chemical Fokker-Planck equation (CFPE). The latter is a continuum approximation of the discrete CME approach. We here show…
One of the main challenges in diffusion-based molecular communication is dealing with the non-linearity of reaction-diffusion chemical equations. While numerical methods can be used to solve these equations, a change in the input signals or…
This paper focuses on molecular communication (MC) systems where the signaling molecules may participate in a reversible bimolecular reaction in the channel. The motivation for studying these MC systems is that they can realize the concept…
Mathematical modeling is now used commonly in the analysis of signaling networks. With advances in high resolution microscopy, the spatial location of different signaling molecules and the spatio-temporal dynamics of signaling microdomains…
The notion of entropy is shared between statistics and thermodynamics, and is fundamental to both disciplines. This makes statistical problems particularly suitable for reaction network implementations. In this paper we show how to perform…
We investigate theoretically the stochastic dynamics of Resonance Electronic Energy Transfer (RET), in a bi-dimensional overexcited ensemble of donor and acceptor molecules. We find that, after initial optical excitation of all the donors,…
Information delivery using chemical molecules is an integral part of biology at multiple distance scales and has attracted recent interest in bioengineering and communication. The collective signal strength at the receiver (i.e., the…
Turing patterns can be observed in reaction-diffusion systems where chemical species have different diffusion constants. In recent years, several studies investigated the effects of noise on Turing patterns and showed that the parameter…
A molecular communication channel is determined by the received signal. Received signal models form the basis for studies focused on modulation, receiver design, capacity, and coding depend on the received signal models. Therefore, it is…
The reaction-diffusion master equation (RDME) is a model that allows for efficient on-lattice simulation of spatially resolved stochastic chemical kinetics. Compared to off-lattice hard-sphere simulations with Brownian Dynamics (BD) or…