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Diffusion maps approximate the generator of Langevin dynamics from simulation data. They afford a means of identifying the slowly-evolving principal modes of high-dimensional molecular systems. When combined with a biasing mechanism,…

Data Analysis, Statistics and Probability · Physics 2020-07-01 Zofia Trstanova , Ben Leimkuhler , Tony Lelièvre

The molecular motion in heterogeneous media displays anomalous diffusion by the mean-squared displacement $\langle X^2(t) \rangle = 2 D t^\alpha$. Motivated by experiments reporting populations of the anomalous diffusion parameters $\alpha$…

Biological Physics · Physics 2025-10-09 Yann Lanoiselée , Gianni Pagnini , Agnieszka Wyłomańska

This paper, in French, describes a series of completely different behaviours of the mechanics of granular matter, which are obtained experimentally using periodic forcing at different amplitude, frequency and orientation. It starts with the…

Soft Condensed Matter · Physics 2007-05-23 P. Evesque

Last year in [Phys. Rev. E 102, 042121 (2020)] the authors studied an overdamped dynamics of nonequilibrium noise driven Brownian particle dwelling in a spatially periodic potential and discovered a novel class of Brownian, yet non-Gaussian…

Statistical Mechanics · Physics 2021-12-22 Karol Białas , Jakub Spiechowicz

Diffusive dynamics abound in nature and have been especially studied in physical, biological, and financial systems. These dynamics are characterised by a linear growth of the mean squared displacement (MSD) with time. Often, the conditions…

Statistical Mechanics · Physics 2025-11-14 Alvaro Lanza , Xiang Qu , Stefano Bo

We study self-diffusion and sedimentation in colloidal suspensions of nearly-hard spheres using the multiparticle collision dynamics simulation method for the solvent with a discrete mesh model for the colloidal particles (MD+MPCD). We…

Soft Condensed Matter · Physics 2022-01-26 Yashraj M. Wani , Penelope Grace Kovakas , Arash Nikoubashman , Michael P. Howard

Chemical reactions inside cells are generally considered to happen within fixed-size compartments. Needless to say, cells and their compartments are highly dynamic. Thus, such stringent assumptions may not reflect biochemical reality, and…

Quantitative Methods · Quantitative Biology 2016-02-17 Atiyo Ghosh , Tatiana T. Marquez-Lago

We present a model of anomalous diffusion consisting of an ensemble of particles undergoing homogeneous Brownian motion except for confinement by randomly placed reflecting boundaries. For power-law distributed compartment sizes, we…

Soft Condensed Matter · Physics 2015-06-09 Gerald John Lapeyre

The prediction of diffusion in solids is necessary to understand the microstructure evolution in materials out of equilibrium. Although one can reasonably predict diffusive transport coefficients using atomistic methods, these approaches…

Materials Science · Physics 2025-08-07 Jacob Jeffries , Emilio Mendoza Reyes , Fadi Abdeljawad , Murray Daw , Enrique Martinez

It has recently been shown that there are substantial differences in the regularity behavior of the empirical process based on scalar diffusions as compared to the classical empirical process, due to the existence of diffusion local time.…

Probability · Mathematics 2011-05-25 Angelika Rohde , Claudia Strauch

We consider the time dependent dispersion properties of overdamped tracer particles diffusing in a one dimensional periodic potential under the influence of an additional constant tilting force $F$. The system is studied in the region where…

Statistical Mechanics · Physics 2017-02-01 T. Guérin , D. S. Dean

We perform molecular dynamic simulations of liquid nanoparticles deposited on a disordered substrate. The motion of the nanoparticle is characterised by a 'stick and roll' diffusive process. Long simulation times ($\simeq \mu s$), analysis…

Materials Science · Physics 2009-11-10 F. Celestini

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…

Soft Condensed Matter · Physics 2008-10-15 P. Henseler , A. Erbe , M. Köppl , P. Leiderer , P. Nielaba

Elastic wave propagation provides a noninvasive way to probe granular materials. The discrete element method using particle configuration as input, allows a micromechanical interpretation on the acoustic response of a given granular system.…

Geophysics · Physics 2018-08-28 Hongyang Cheng , Stefan Luding , Kuniyasu Saitoh , Vanessa Magnanimo

Depending on their mechanism of self-propulsion, active particles can exhibit a time-dependent, often periodic, propulsion velocity. The precise propulsion velocity profile determines their mean square displacement and their effective…

Soft Condensed Matter · Physics 2024-05-06 Arnau Jurado Romero , Carles Calero , Rossend Rey

We study the diffusiophoretic self-propulsion of a colloidal catalytic particle due to a surface chemical reaction in a vicinity of a solid wall. Diffusiophoresis is a chemico-mechanical transduction mechanism in which a concentration…

Soft Condensed Matter · Physics 2016-06-22 Ali Mozaffari , Nima Sharifi-Mood , Joel Koplik , Charles Maldarelli

We study both experimentally and theoretically the dynamics of chemically self-propelled Janus colloids moving atop a two-dimensional crystalline surface. The surface is a hexagonally close-packed monolayer of colloidal particles of the…

Soft Condensed Matter · Physics 2017-12-19 Udit Choudhury , Arthur V. Straube , Peer Fischer , John G. Gibbs , Felix Höfling

We investigate both ensemble and time-averaged mean-squared displacements of particles in a polydisperse granular system in a homogeneous cooling state. The system contains an arbitrary number of species of different sizes and masses. The…

Soft Condensed Matter · Physics 2024-09-20 Anna S. Bodrova , Alexander I. Osinsky

Diffusion of a tagged particle near a constraining biological surface is examined numerically by modeling the surface-water interaction by an effective potential. The effective potential is assumed to be given by an asymmetric double well…

Soft Condensed Matter · Physics 2007-05-23 Arnab Mukherjee , Biman Bagchi

Wavefunction collapse models modify Schr\"odinger's equation so that it describes the collapse of a superposition of macroscopically distinguishable states as a dynamical process. This provides a basis for the resolution of the quantum…

Quantum Physics · Physics 2014-11-26 Daniel Bedingham , Hendrik Ulbricht