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A Poisson-Nernst-Planck-Fermi (PNPF) theory is developed for studying ionic transport through biological ion channels. Our goal is to deal with the finite size of particle using a Fermi like distribution without calculating the forces…

Biological Physics · Physics 2015-06-23 Jinn-Liang Liu , Bob Eisenberg

The evolution of an initially prepared distribution of micron sized colloidal particles, trapped at a fluid interface and under the action of their mutual capillary attraction, is analyzed by using Brownian dynamics simulations. At a…

Soft Condensed Matter · Physics 2011-11-29 J. Bleibel , A. Dominguez , M. Oettel , S. Dietrich

Dynamics of a Brownian particle in an asymmetric micro-channel that is subjected to an external oscillating force is numerically analyzed. In addition to the elastic collisions with the walls that are kind of short range interactions, the…

Soft Condensed Matter · Physics 2015-06-23 B. Golshaei , A. Najafi

We investigate the transport diffusivity of artificial microswimmers, a.k.a. Janus particles, moving in a sinusoidal channel in the absence of external biases. Their diffusion constant turns out to be quite sensitive to the self-propulsion…

Soft Condensed Matter · Physics 2015-01-19 Xue Ao , Pulak Kumar Ghosh , Yunyun Li , Gerhard Schmid , Peter Hänggi , Fabio Marchesoni

We study how the complex interplay between roughness, inertia, and diffusion controls the tracer transport in rough channels. We first simulate the flow and tracer transport over wide ranges of channel roughness, Reynolds number ($Re$), and…

Fluid Dynamics · Physics 2021-02-03 Seonkyoo Yoon , Peter K. Kang

Transport and dispersion of active particles in structured environments such as corrugated channels and porous media are important for the understanding of both natural and engineered active systems. Owing to their continuous…

Soft Condensed Matter · Physics 2024-10-16 Zhiwei Peng

We propose a theoretical model which relies on the generalized Langevin equation and may account for various dynamical features of the thermal motion of organelles, vesicles or macromolecules in viscoelastic media such as polymer networks.…

Soft Condensed Matter · Physics 2020-01-03 Denis S. Grebenkov , Mahsa Vahabi , Elena Bertseva , Laszlo Forro , Sylvia Jeney

Among all fluids, water has always been of special concern for scientists from a broad variety of research fields due to its rich behavior. In particular, some questions remain unanswered nowadays concerning the temperature dependence of…

Chemical Physics · Physics 2022-07-06 Cecilia Herrero , Michela Pauletti , Gabriele Tocci , Marcella Iannuzzi , Laurent Joly

Due to the complex interplay between surface adsorption and hydrodynamic interactions, representative microscopic mechanisms of colloidal membrane fouling are still not well understood. Numerical simulations overcome experimental…

Computational Physics · Physics 2018-03-22 Johannes Lohaus , Yannic Martin Perez , Matthias Wessling

A density functional theory for colloidal dynamics is presented which includes hydrodynamic interactions between the colloidal particles. The theory is applied to the dynamics of colloidal particles in an optical trap which switches…

Soft Condensed Matter · Physics 2009-11-13 M. Rex , H. Loewen

We investigate the transport of Brownian particles in a two-dimensional potential under the action of a uniform external force. The potential is periodic in one direction and confines the particle to a narrow channel of varying…

Statistical Mechanics · Physics 2016-05-04 Xinli Wang , German Drazer

A quantitative relationship between the diffusion coefficient $D$ of a tagged particle in a liquid and the entropy $S$ of that liquid has long been sought, as it would allow entropy to be inferred directly from diffusion measurements and…

Statistical Mechanics · Physics 2025-09-25 Nayana Venkatareddy , Mohd Moid , Prabal K. Maiti , Biman Bagchi

Transport surrounding is full of all kinds of fields, like particle potential, external potential. Under these conditions, how elements work and how position and momentum redistribute in the diffusion? For enriching the Fick law in…

Soft Condensed Matter · Physics 2017-08-02 Jian-hui He , Jia-le Wen , Pei-rong Chen , Dong-qin Zheng , Wei-rong Zhong

We used single-molecule tracking to probe the local rheology of interfacial water. Fluorescent rhodamine molecules were tracked on silica surfaces as a function of ambient relative humidity, which controlled the thickness of condensed water…

Soft Condensed Matter · Physics 2020-01-20 Raphael Sarfati , Daniel K. Schwartz

Hydrodynamic noise is the Gaussian process that emerges at larges scales of space and time in many-body systems. It is justified by the central limit theorem, and represents degrees of freedom forgotten when projecting coarse-grained…

Statistical Mechanics · Physics 2026-04-15 Benjamin Doyon

In our recent work on concentrated suspensions of uniformly porous colloidal spheres with excluded volume interactions, a variety of short-time dynamic properties were calculated, except for the rotational self-diffusion coefficient. This…

Soft Condensed Matter · Physics 2015-05-27 Gustavo C. Abade , Bogdan Cichocki , Maria L. Ekiel-Jezewska , Gerhard Naegele , Eligiusz Wajnryb

In this article we derive and test the fluctuating hydrodynamic description of active particles interacting via taxis and quorum sensing, both for mono-disperse systems and for mixtures of co-existing species of active particles. We compute…

Statistical Mechanics · Physics 2025-01-14 Alberto Dinelli , Jérémy O'Byrne , Julien Tailleur

Molecular Dynamics simulations of water molecules in nanometre sized cylindrical channels connecting two reservoirs show that the permeation of water is very sensitive to the channel radius and to electric polarization of the embedding…

Soft Condensed Matter · Physics 2009-11-07 Rosalind Allen , Simone Melchionna , Jean-Pierre Hansen

Many biological and artificial transport channels function without direct input of metabolic energy during a transport event and without structural rearrangements involving transitions from a 'closed' to an 'open' state. Nevertheless, such…

Subcellular Processes · Quantitative Biology 2009-11-13 Anton Zilman

We derive a closed equation for the empirical concentration of colloidal particles in the presence of both hydrodynamic and direct interactions. The ensemble average of our functional Langevin equation reproduces known deterministic Dynamic…

Statistical Mechanics · Physics 2015-06-19 A. Donev , E. Vanden-Eijnden