Related papers: On the Statistics of Reaction-Diffusion Simulation…

We present a model for diffusion in a molecularly crowded environment. The model consists of random barriers in percolation network. Random walks in the presence of slowly moving barriers show normal diffusion for long times, but anomalous…

Complex biological and physical transport processes are often described through systems of interacting particles. Excluded-volume effects on these transport processes are well studied, however the interplay between volume exclusion and…

Molecular simulations and biophysical experiments can be used to provide independent and complementary insights into the molecular origin of biological processes. A particularly useful strategy is to use molecular simulations as a modelling…

Diffusion models have emerged as powerful generative models in the text-to-image domain. This paper studies their application as observation-to-action models for imitating human behaviour in sequential environments. Human behaviour is…

Describing the diffusion of particles through crowded, confined environments with which they can interact is of considerable biological and technological interest. Under conditions where the confinement dimensions become comparable to the…

The transport and chemical reactions of solutes are modelled as a cellular automaton in which molecules of different species perform a random walk on a regular lattice and react according to a local probabilistic rule. The model describes…

The existing literature on stochastic simulation of chemical reaction networks has a tendency to move as quickly as possible to the abstract formulation of the stochastic dynamics in terms of probabilities based on the concept of 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…

Diffusion is a fundamental phenomenon that occurs ubiquitously in nature and remains the subject of continuous research interest. Understanding diffusion is a key to understanding leaving systems. In this Chapter, I discuss diffusion of…

We study a system of diffusing point particles in which any triplet of particles reacts and is removed from the system when the relative proximity of the constituent particles satisfies a predefined condition. Proximity-based reaction…

Dynamical systems theory provides powerful methods to extract effective macroscopic dynamics from complex systems with slow modes and fast modes. Here we derive and theoretically support a macroscopic, spatially discrete, model for a class…

Diffusion of colloidal particles in a complex environment such as polymer networks or biological cells is a topic of high complexity with significant biological and medical relevance. In such situations, the interaction between the…

This survey paper focuses on modulation aspects of molecular communication, an emerging field focused on building biologically-inspired systems that embed data within chemical signals. The primary challenges in designing these systems are…

At finite concentrations of reacting molecules, kinetics of diffusion-controlled reactions is affected by intra-reactant interactions. As a result, multi-particle reaction statistics cannot be deduced from single-particle results. Here we…

In this paper, we propose adding enzymes to the propagation environment of a diffusive molecular communication system as a strategy for mitigating intersymbol interference. The enzymes form reaction intermediates with information molecules…

Active transport such as fluid flow is sought in molecular communication to extend coverage, improve reliability, and mitigate interference. Flow models are often over-simplified, assuming one-dimensional diffusion with constant drift.…

The activity of biological cells is primarily based on chemical reactions and typically modeled as a reaction-diffusion system. Cells are, however, highly crowded with macromolecules, including a variety of molecular machines such as…

A variety of simulation methodologies have been used for modeling reaction-diffusion dynamics -- including approaches based on Differential Equations (DE), the Stochastic Simulation Algorithm (SSA), Brownian Dynamics (BD), Green's Function…

Reaction diffusion equations have been used to model a wide range of biological phenomenon related to population spread and proliferation from ecology to cancer. It is commonly assumed that individuals in a population have homogeneous…

In this paper, we apply dimensional analysis to study a diffusive molecular communication system that uses diffusing enzymes in the propagation environment to mitigate intersymbol interference. The enzymes bind to information molecules and…