Related papers: Diffusive dynamics of contact formation in disorde…
Using molecular dynamics simulation of a standard bead-spring model we investigate the density crossover scaling of strictly two-dimensional self-avoiding polymer chains focusing on properties related to the contact exponent set by the…
We present an investigation into diffusion models for molecular generation, with the aim of better understanding how their predictions compare to the results of physics-based calculations. The investigation into these models is driven by…
The dispersed phase in liquid-liquid emulsions and air-liquid mixtures can often be fragmented into smaller sizes by the surrounding turbulent carrier phase. The critical parameter that controls this process is the breakup frequency, which…
We consider a theoretical model for a binary mixture of colloidal particles and spherical emulsion droplets. The hard sphere colloids interact via additional short-ranged attraction and long-ranged repulsion. The droplet-colloid interaction…
We consider a basic one-dimensional model of diffusion which allows to obtain a diversity of diffusive regimes whose speed depends on the moments of the per-site trapping time. This model is closely related to the continuous time random…
We study compressible fluid flow in narrow two-dimensional channels using a novel molecular dynamics simulation method. In the simulation area, an upstream source is maintained at constant density and temperature while a downstream…
We propose an approach that links density functional theory (DFT) and molecular dynamics (MD) simulation to study fluid behavior in nanopores in contact with bulk (macropores). It consists of two principal steps. First, the theoretical…
In structure-based models of proteins, one often assumes that folding is accomplished when all contacts are established. This assumption may frequently lead to a conceptual problem that folding takes place in a temperature region of very…
We use molecular dynamics simulations to study the behavior of a compressible Lennard-Jones fluid in simple shear flow in a two-dimensional nanochannel. The system is equilibrated in the fluid phase close to the triple point at which gas,…
We present a field theoretic renormalization group study for the critical behaviour of a uniformly driven diffusive system with quenched disorder, which is modelled by different kinds of potential barriers between sites. Due to their…
In this paper we propose and validate a multiscale model for the description of particle diffusion in presence of trapping boundaries. We start from a drift-diffusion equation in which the drift term describes the effect of bubble traps,…
How many times a diffusing molecule can permeate across a membrane or be adsorbed on a substrate? We employ the encounter-based approach to find the statistics of adsorption or permeation events for molecular diffusion in a general…
Many essential cellular processes, including cell division and the establishment of cell polarity during embryogenesis, are regulated by pattern-forming proteins. These proteins often need to bind to a substrate, such as the cell membrane,…
We use molecular dynamics simulations to study the evaporation of particle-laden droplets on a heated surface. The droplets are composed of a Lennard-Jones fluid containing rigid particles which are spherical sections of an atomic lattice,…
A reduced model, which can fold both helix and sheet structures, is proposed to study the problem of protein folding. The goal of this model is to find an unbiased effective potential that has included the effects of water and at the same…
We show that intensity of a wave created by a source embedded inside a three-dimensional disordered medium exhibits a non-universal space-time correlation which depends explicitly on the short-distance properties of disorder, source size,…
To sensitively test scaling in the 2D XY model quenched from high-temperatures into the ordered phase, we study the difference between measured correlations and the (scaling) results of a Gaussian-closure approximation. We also directly…
Abridged abstract: Inert interactions between randomly moving entities and spatial disorder play a crucial role in quantifying the diffusive properties of a system. These interactions affect only the movement of the entities, and examples…
When a chromophore interacts with titrable molecular sites, the modeling of its photophysical properties requires to take into account all their possible protonation states. We have developed a multi-scale protocol, based on constant-pH…
We consider a thin droplet that spreads over a flat, horizontal and chemically heterogeneous surface. The droplet is subjected to changes in its volume though a prescribed, arbitrary spatiotemporal function, which varies slowly and vanishes…