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Brownian Dynamics algorithms are widely used for simulating soft-matter and biochemical systems. In recent times, their application has been extended to the simulation of coarse-grained models of cellular networks in simple organisms. In…
We consider the trapping reaction, $A+B\to B$, where $A$ and $B$ particles have a diffusive dynamics characterized by diffusion constants $D_A$ and $D_B$. The interaction with $B$ particles can be formally incorporated in an effective…
We perform a comprehensive study of noise-induced effects in a stochastic model of reaction-diffusion type, describing nano-structured thin films growth at condensation. We introduce an external flux of adsorbate between neighbour…
Most biochemical reactions in living cells rely on diffusive search for target molecules or regions in a heterogeneous overcrowded cytoplasmic medium. Rapid re-arrangements of the medium constantly change the effective diffusivity felt…
Electrogenerated gas nanobubbles strongly influence the performance of electrochemical energy-conversion systems, yet their nucleation and early evolution remain poorly understood due to limitations of existing experimental and…
Micrometer-sized objects are widely known to exhibit chemically-driven motility in systems away from equilibrium. Experimental observation of reaction-induced motility or enhancement in diffusivity at the much shorter length scale of small…
A theoretical treatment of deeply supercooled liquids is difficult because their properties emerge from spatial inhomogeneities that are self-induced, transient, and nanoscopic. I use computer simulations to analyse self-induced static and…
We derive the stochastic model of plasma-condensate systems by taking into account anisotropy in transference of adatoms between neighbor layers and by introducing fluctuations of adsorbate flux. We show, that by varying the fluctuation's…
Metallic nanoparticles embedded in stimuli-responsive polymers can be regarded as nanoreactors since their catalytic activity can be changed within wide limits: the physicochemical properties of the polymer network can be tuned and switched…
A stochastic model for the dynamics of enzymatic catalysis in explicit, effective solvents under physiological conditions is presented. Analytically-computed first passage time densities of a diffusing particle in a spherical shell with…
Here, steady-state reaction networks are inspected from the viewpoint of individual tagged molecules jumping among their chemical states upon the occurrence of reactive events. Such an agent-based viewpoint is useful for selectively…
We study the dynamics of simple reactions where the chemical species are confined on a general, time-modulated surface, and subjected to externally-imposed stirring. The study of these inhomogeneous effects requires a model based on a…
We study a model for unimolecular reaction on a supported catalyst including reactant diffusion and desorption, using analytical methods and scaling concepts. For rapid reactions, enhancing surface diffusion or increasing particle size…
A finite-time fluctuation theorem is proved for the diffusion-influenced surface reaction A<->B in a domain with any geometry where the species A and B undergo diffusive transport between the reservoir and the catalytic surface. A…
We consider a class of bulk-surface reaction-adsorption-diffusion systems, i.e. a coupled systems of reaction-diffusion systems on a bounded domain $\Omega \subseteq \mathbb{R}^d$ (bulk phase) and its boundary $\Sigma = \partial \Omega$…
This study combines broadband dielectric spectroscopy (BDS) experiments with molecular dynamics (MD) simulations to investigate the influence of nanoparticle (NP) inclusions on pretransitional phenomena in a liquid crystal (LC) host. We…
Many cellular and subcellular biological processes can be described in terms of diffusing and chemically reacting species (e.g. enzymes). Such reaction-diffusion processes can be mathematically modelled using either deterministic…
Surface effects could play a dominant role in modifying the natural liquid order. In some cases, the effects of the surface interactions can propagate inwards, and even can interfere with a similar propagation from opposite surfaces. This…
Molecular-scale interactions between solvated macromolecules and solid surfaces govern a large number of processes, from biology to engineering. Yet, despite extensive characterization at the macroscopic level, our molecular understanding…
The behavior of a confined spherical symmetric anomalous fluid under high external pressure was studied with Molecular Dynamics simulations. The fluid is modeled by a ore-softened potential with two characteristic length scales, which in…