Introducing memory in coarse-grained molecular simulations

V Klippenstein, M Tripathy, G Jung… - The Journal of …, 2021 - ACS Publications
Preserving the correct dynamics at the coarse-grained (CG) level is a pressing problem in
the development of systematic CG models in soft matter simulation. Starting from the seminal …

Microrheology of colloidal systems

AM Puertas, T Voigtmann - Journal of Physics: Condensed …, 2014 - iopscience.iop.org
Microrheology was proposed almost twenty years ago as a technique to obtain rheological
properties in soft matter from the microscopic motion of colloidal tracers used as probes …

Advances in the microrheology of complex fluids

TA Waigh - Reports on Progress in Physics, 2016 - iopscience.iop.org
New developments in the microrheology of complex fluids are considered. Firstly the
requirements for a simple modern particle tracking microrheology experiment are …

Iterative reconstruction of memory kernels

G Jung, M Hanke, F Schmid - Journal of chemical theory and …, 2017 - ACS Publications
In recent years, it has become increasingly popular to construct coarse-grained models with
non-Markovian dynamics to account for an incomplete separation of time scales. One …

Generalized Langevin dynamics: construction and numerical integration of non-Markovian particle-based models

G Jung, M Hanke, F Schmid - Soft matter, 2018 - pubs.rsc.org
We propose a generalized Langevin dynamics (GLD) technique to construct non-Markovian
particle-based coarse-grained models from fine-grained reference simulations and to …

Non-Markovian out-of-equilibrium dynamics: A general numerical procedure to construct time-dependent memory kernels for coarse-grained observables

H Meyer, P Pelagejcev, T Schilling - Europhysics Letters, 2020 - iopscience.iop.org
We present a numerical method to compute non-equilibrium memory kernels based on
experimental data or molecular dynamics simulations. The procedure uses a recasting of the …

[HTML][HTML] Cross-correlation corrected friction in (generalized) Langevin models

V Klippenstein, NFA van der Vegt - The Journal of Chemical Physics, 2021 - pubs.aip.org
We propose a route for parameterizing isotropic (generalized) Langevin [(G) LE] thermostats
with the aim to correct the dynamics of coarse-grained (CG) models with pairwise …

[HTML][HTML] Microrheology analysis in molecular dynamics simulations: Finite box size correction

JG Ethier, P Nourian, R Islam, R Khare… - Journal of …, 2021 - pubs.aip.org
In single-particle microrheology, the viscoelastic properties of a complex fluid can be
extracted using the generalized Stokes–Einstein (GSE) relation by embedding a micrometer …

Microrheology, advances in methods and insights

Q Xia, H Xiao, Y Pan, L Wang - Advances in Colloid and Interface Science, 2018 - Elsevier
Microrheology is an emerging technique that probes mechanical response of soft material at
micro-scale. Generally, microrheology technique can be divided into active and passive …

[HTML][HTML] Energy fluctuations of a Brownian particle freely moving in a liquid

JR Gomez-Solano - Physica A: Statistical Mechanics and its Applications, 2024 - Elsevier
We study the statistical properties of the variation of the kinetic energy of a spherical
Brownian particle that freely moves in an incompressible fluid at constant temperature …