Related papers: Diffusive dynamics of contact formation in disorde…
Intrachain contact formation rates, fundamental to the dynamics of biopolymer self-organization such as protein folding, can be monitored in the laboratory through fluorescence quenching measurements. The common approximations for the…
New theoretical and numerical analysis of the one-dimensional contact process with quenched disorder are presented. We derive new scaling relations, different from their counterparts in the pure model, which are valid not only at the…
A Markov state model is a powerful tool that can be used to track the evolution of populations of configurations in an atomistic representation of a protein. For a coarse-grained linear chain model with discontinuous interactions, the…
The motion of the three-phase contact line between two immiscible fluids and a solid surface arises in a variety of wetting phenomena and technological applications. One challenge in continuum theory is the effective representation of…
Synthetic polymers have a distribution of chain lengths which can be characterized by dispersity, D. Macroscopic properties of polymers are influenced by chain mobility in the melt and manipulating D can significantly impact these…
Quenched disorder in absorbing phase transitions can disrupt the structure and symmetry of reaction-diffusion processes, offering a more accurate mapping to real physical systems. We developed a temporally quenched disorder method in the…
The phase transition of the one-dimensional, diffusive pair contact process (PCPD) is investigated by N cluster mean-field approximations and high precision simulations. The N=3,4 cluster approximations exhibit smooth transition line to…
The absorbing-state transition in the three-dimensional contact process with and without quenched randomness is investigated by means of Monte-Carlo simulations. In the clean case, a reweighting technique is combined with a careful…
The study of interactions between biomimetic membranes and micron-sized particles is crucial for understanding various biological processes. Here, we control microparticle spontaneous engulfment by giant lipid vesicles by tuning particle…
We study the effect of quenched disorder on nonequilibrium systems of interacting particles, specifically, driven diffusive lattice gases with spatially disordered jump rates. The exact steady-state measure is found for a class of models…
We develop a general analysis of the diffusive dynamics of polydisperse polymers in the presence of chemical potential gradients, within the context of the tube model (with all species entangled). We obtain a set of coupled dynamical…
The authors study the short-time dynamics of helix-forming polypeptide chains using an all-atom representation of the molecules and an implicit solvation model to approximate the interaction with the surrounding solvent. The results confirm…
Fluid phase equilibria involving nano-dispersed phases, where at least one of the coexisting phases is confined to a small volume, are investigated by molecular dynamics simulation. Complementing previous studies on nanoscopic droplets,…
We study critical spreading dynamics in the two-dimensional contact process (CP) with quenched disorder in the form of random dilution. In the pure model, spreading from a single particle at the critical point $\lambda_c$ is characterized…
We have studied the critical properties of the contact process on a square lattice with quenched site dilution by Monte Carlo simulations. This was achieved by generating in advance the percolating cluster, through the use of an appropriate…
Long DNA molecules can be mapped by cutting them with restriction enzymes inside a narrow channel. Once cut, the individual fragments thus produced move away from each other due to diffusion and entropic effects. We investigate how long it…
It has long been asserted that proteins like transcription factors may locate their target in DNA sequences at rates that surpass by several orders of magnitude the three-dimensional diffusion limit thank to facilitated diffusion, that is…
Dynamic wetting poses a well-known challenge in classical sharp-interface formulation as the no-slip wall condition leads to a contact line singularity that is typically regularized with a Navier boundary condition, often requiring…
We report a numerical study of the diffusiophoresis of short polymers using non-equilibrium molecular dynamics simulations. More precisely, we consider polymer chains in a fluid containing a solute which has a concentration gradient, and…
We investigate the connections between microscopic chaos, defined on a dynamical level and arising from collisions between molecules, and diffusion, characterized by a mean square displacement proportional to the time. We use a number of…