Related papers: Single file dynamics in soft materials
The dynamics of entrainment of finite-size heavy particles in a turbulent open channel flow over a smooth surface are analyzed. Three types of simulations, namely with freely moving, rotation-constrained, and spanwise-motion-constrained…
We investigate single-particle diffusion in a two-state Langevin model where the friction coefficient randomly switches between low-friction (liquid-like) and high-friction (glassy-like) states. The dynamics are governed by the ratio…
We characterize the dynamic non-equilibrium steady state behavior of active particles using density fluctuations in the system. We analyze the effective local density around a particle in the steady state and numerically calculate its mean,…
Single-molecule biophysics has transformed our understanding of the fundamental molecular processes involved in living biological systems, but also of the fascinating physics of life. Far more exotic than a collection of exemplars of soft…
Single-file transport, arising in quasi one-dimensional geometries where particles cannot pass each other, is characterized by the anomalous dynamics of a probe, notably its response to an external force. In these systems, the motion of…
We present an implicit statistical model for the steric effect on the potential of mean force (PMF) of a molecule diffusing through a flexible nanochannel of varying size. The average cross sectional area profile of the channel and the…
A simple theory of ion permeation through a channel is presented, in which diffusion occurs according to Fick's law and drift according to Ohm's law, in the electric field determined by all the charges present. This theory accounts for…
A new phase field crystal (PFC) type theory is presented, which accounts for the full spectrum of solid-liquid-vapor phase transitions within the framework of a single density order parameter. Its equilibrium properties show the most…
Biological molecules, like all active matter, use free energy to generate force and motion which drive them out of thermal equilibrium, and undergo inherent dynamic interconversion between metastable free energy states separated by levels…
Simulations of over $10^3$ hydrodynamically coupled solid spheres are performed to investigate collective motion of linear trains and regular square arrays of particles suspended in a fluid bounded by two parallel walls. Our novel…
The behavior of particles driven through a narrow constriction is investigated in experiment and simulation. The system of particles adapts to the confining potentials and the interaction energies by a self-consistent arrangement of the…
Sparse data is fundamental to scientific simulations in biology and physics, from single-cell gene expression to particle calorimetry, where exact zeros encode physical absence rather than weak signal. However, existing diffusion models…
A new Chemo-Dynamical Smoothed Particle Hydrodynamic (CD-SPH) code is presented. The disk galaxy is described as a multi-fragmented gas and star system, embedded in a cold dark matter halo with a rigid potential field. The star formation…
The diffusion of active microscopic organisms in complex environments plays an important role in a wide range of biological phenomena from cell colony growth to single organism transport. Here, we investigate theoretically and…
The movement of motor particles consisting of one or several molecular motors bound to a cargo particle is studied theoretically. The particles move on patterns of immobilized filaments. Several patterns are described for which the motor…
We study the dynamics of a tagged particle in an environment of point Brownian particles with hard-core interactions in an infinite one dimensional channel (a single-file model). In particular we examine the influence of initial conditions…
This work presents the mathematical and computational aspects of a smooth dissipative particle dynamics with dynamic virtual particle allocation method (SDPD-DV) for modeling and simulation of mesoscopic fluids in wall-bounded domains. The…
We follow the trajectories of phase singularities at nulls of intensity in the speckle pattern of waves transmitted through random media as the frequency of the incident radiation is scanned in microwave experiments and numerical…
We study the single file diffusion problem on a one-dimensional lattice with a self-similar distribution of hopping rates. We find that the time dependence of the mean-square displacement of both a tagged particle and the center of mass of…
Generative diffusion models have achieved remarkable success in producing high-quality images. However, these models typically operate in continuous intensity spaces, diffusing independently across pixels and color channels. As a result,…