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Recently, hybrid models have emerged that combine microscopic and mesoscopic regimes in a single stochastic reaction-diffusion simulation. Microscopic simulations track every individual molecule and are generally more accurate. Mesoscopic…
We present the spatial regime conversion method (SRCM), a novel hybrid modelling framework for simulating reaction-diffusion systems that adaptively combines stochastic discrete and deterministic continuum representations. Extending the…
In this paper an analytical model is introduced to describe the impulse response of the diffusive channel between a pointwise transmitter and a given fully-absorbing (FA) receiver in a molecular communication (MC) system. The presence of…
Several stochastic simulation algorithms (SSAs) have been recently proposed for modelling reaction-diffusion processes in cellular and molecular biology. In this paper, two commonly used SSAs are studied. The first SSA is an on-lattice…
Molecular communication (MC) enables information exchange at the nano- and microscale, with applications in areas like drug delivery and health monitoring. These event-driven scenarios often require alternatives to traditional transmission.…
Cells process external and internal signals through chemical interactions. Cells that constitute the immune system (e.g., antigen presenting cell, T-cell, B-cell, mast cell) can have different functions (e.g., adaptive memory, inflammatory…
We develop a statistical toolbox for a quantitative model evaluation of stochastic reaction-diffusion systems modeling space-time evolution of biophysical quantities on the intracellular level. Starting from space-time data $X_N(t,x)$, as,…
Quantal diffusion mechanism of nucleon exchange is studied in the central collisions of several symmetric heavy-ion collisions in the framework of the Stochastic Mean-Field (SMF) approach. Since at bombarding energies below the fusion…
This paper studies the impact of a transmitter's molecule generation process on the capacity of a concentration based Molecular Communication (MC) system. Constraints caused by the molecule generation process affect the availability of the…
Molecular communication (MC) is a promising paradigm for applications where traditional electromagnetic communications are impractical. However, decoding chemical signals, especially in multi-transmitter systems, remains a key challenge due…
Stochasticity is a key characteristic of intracellular processes such as gene regulation and chemical signalling. Therefore, characterising stochastic effects in biochemical systems is essential to understand the complex dynamics of living…
We used various analytical and numerical techniques to elucidate signal propagation in a small enzymatic cascade which is subjected to external and internal noise. The nonlinear character of catalytic reactions, which underlie protein…
Molecular communication (MC) is a paradigm that employs molecules as information transmitters, hence, requiring unconventional transceivers and detection techniques for the Internet of Bio-Nano Things (IoBNT). In this study, we provide a…
Our brain is a complex information processing network in which the nervous system receives information from the environment to quickly react to incoming events or learns from experience to sharp our memory. In the nervous system, the brain…
Simulation of biomolecular networks is now indispensable for studying biological systems, from small reaction networks to large ensembles of cells. Here we present a novel approach for stochastic simulation of networks embedded in the…
In molecular communications, the direct detection of signaling molecules may be challenging due to a lack of suitable sensors and interference in the environment. Motivated by research in molecular biology, we investigate an indirect…
Molecular signals are abundant in engineering and biological contexts, and undergo stochastic propagation in fluid dynamic channels. The received signal is sensitive to a variety of input and channel parameter variations. Currently we do…
We present a novel formulation for biochemical reaction networks in the context of signal transduction. The model consists of input-output transfer functions, which are derived from differential equations, using stable equilibria. We select…
This paper considers a diffusion-based molecular communication system where the transmitter uses Reaction Shift Keying (RSK) as the modulation scheme. We focus on the demodulation of RSK signal at the receiver. The receiver consists of a…
In this work a stochastic model of gaseous transfer in polymer/CNT nanocomposites is presented. The model takes into account interfacial areas, i.e. polymer depletion regions. The local regime of transport is controlled by the density of…