Related papers: Confinement determines transport of a reaction-dif…
The effect of a diffusivity edge is studied in a system of scalar active matter confined by a periodic potential and driven by an externally applied force. We find that this system shows qualitatively distinct stationary regimes depending…
The physics of diffusion phenomena in nano and micro channels has attracted a lot of attention in recent years, due to its close connection with many technological, medical and industrial applications. In the present paper we employ a…
Mixing fronts, where fluids of different chemical compositions mix with each other, are typically subjected to velocity gradients, ranging from the pore scale to the catchment scale due to permeability variations and flow line geometries. A…
The empirical velocity of a reaction-diffusion front, propagating into an unstable state, fluctuates because of the shot noises of the reactions and diffusion. Under certain conditions these fluctuations can be described as a diffusion…
In many biological systems, the movement of individual agents is commonly characterized as having multiple qualitatively distinct behaviors that arise from various biophysical states. This is true for vesicles in intracellular transport,…
The burning plasma performance is limited by the confinement of the superalfvenic fusion products such as alpha particles and the auxiliary heating ions capable of exciting the Alfv\'enic eigenmodes (AEs). In this work the effect of AEs on…
A fractional reaction-diffusion equation is derived from a continuous time random walk model when the transport is dispersive. The exit from the encounter distance, which is described by the algebraic waiting time distribution of jump…
Confinement can significantly alter fluid properties, offering potential for specific technological applications. However, achieving precise control over the structural complexity of confined fluids and soft matter remains challenging, as…
We study the effect of confinement on the three-dimensional linear instability of fastly rotating two-dimensional turbulent flows. Using the large scale friction to model the effect of top and bottom boundaries, we study the onset of…
We investigate the nonequilibrium dynamics of semiflexible polymers driven by motor proteins (MPs) in two-dimensional motility assays under harmonic confinement. Using a coarse-grained agent-based model that incorporates stochastic motor…
Using dynamical density functional theory we calculate the speed of solidification fronts advancing into a quenched two-dimensional model fluid of soft-core particles. We find that solidification fronts can advance via two different…
We present a plane-wave basis set implementation of charge constrained density functional molecular dynamics (CDFT-MD) for simulation of electron transfer reactions in condensed phase systems. Following earlier work of Wu et al. Phys. Rev.…
The Ribosome Flow Model (RFM) describes the unidirectional movement of interacting particles along a one-dimensional chain of sites. As a site becomes fuller, the effective entry rate into this site decreases. The RFM has been used to model…
Mass conservation in chemical species appears in a broad class of reaction-diffusion systems (RDs) and is known to bring about coarsening of the pattern in chemical concentration. Recent theoretical studies on RDs with mass conservation…
Rugged (or, rough) energy landscape (REL) with spatially distributed maxima and minima are often employed in applications of physics, chemistry and biology (enzyme kinetics, protein folding, diffusion in disordered solids, transport in…
Bacterial colonies are a well-known example of living active matter, exhibiting collective behaviors such as nematic alignment and collective motion that play an important role in the spread of microbial infections. While the underlying…
Chemical reactions generically require that particles come into contact. In practice, reaction is often imperfect and can necessitate multiple random encounters between reactants. In confined geometries, despite notable recent advances,…
The problem of front propagation in a stirred medium is addressed in the case of cellular flows in three different regimes: slow reaction, fast reaction and geometrical optics limit. It is well known that a consequence of stirring is the…
This paper considers particle propagation in a cylindrical molecular communication channel, e.g. a simplified model of a blood vessel. Emitted particles are influenced by diffusion, flow, and a vertical force induced e.g. by gravity or…
We present Brownian dynamics simulations of the facilitated diffusion of a protein, modelled as a sphere with a binding site on its surface, along DNA, modelled as a semi-flexible polymer. We consider both the effect of DNA organisation in…