RMPCDMD: Simulations of Colloids with Coarse-grained Hydrodynamics,
                        Chemical Reactions and External Fields

Buyl, Pierre de; Mei-Chun, Huang; Deprez, Laurens

doi:10.5334/jors.142

Cited by 5 publications

(9 citation statements)

References 23 publications

(35 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The reaction occurs when the fluid particles crosses the interaction region of the colloid and is executed with a probability p ∈ [0, 1], when the fluid particles exits the interaction region to avoid any discontinuity in the energy [27]. All simulations were performed with the open-source RM-PCDMD software [29,30].…”

Section: Simulation Modelmentioning

confidence: 99%

See 1 more Smart Citation

Passive and active colloidal chemotaxis in a microfluidic channel: mesoscopic and stochastic models

Deprez

Buyl

2017

Soft Matter

Self Cite

View full text Add to dashboard Cite

Chemotaxis is the response of a particle to a gradient in the chemical composition of the environment. While it was originally observed for biological organisms, it is of great interest in the context of synthetic active particles such as nanomotors. Experimental demonstration of chemotaxis for chemically-powered colloidal nanomotors was reported in the literature in the context of chemo-attraction in a still fluid or in a microfluidic channel where the gradient is sustained by a specific inlet geometry. In this work, we use mesoscopic particle-based simulations of the colloid and solvent to demonstrate chemotaxis in a microfluidic channel. On the basis of this particle-based model, we evaluate the chemical concentration profiles in the presence of passive or chemically active colloids, compute the chemotactic force acting upon them and propose a stochastic model that rationalises our findings on colloidal chemotaxis. Our model is also able to explain the results of an earlier simulation work that uses a simpler geometry and to extend its interpretation.

show abstract

Section: Simulation Modelmentioning

confidence: 99%

“…For the dimer nanomotor, the concentration fields depend on the presence of the catalytic sphere of the motor in the same way as for the single active sphere and we reuse Eqs. (27) and (29). The force must be evaluated also on the non-catalytic sphere N where the spherical symmetry does not hold.…”

Section: Dimer Nanomotormentioning

confidence: 99%

Passive and active colloidal chemotaxis in a microfluidic channel: mesoscopic and stochastic models

Deprez

Buyl

2017

Soft Matter

Self Cite

View full text Add to dashboard Cite

show abstract

“…We perform all simulations with the open-source package RM-PCDMD [18,31,32] and provide all the parameter and analysis files in appendix A and in the supplementary information [33].…”

Section: Parametermentioning

confidence: 99%

“…We ran all the simulations with the program single body from the open-source package RMPCDMD for the simulation of passive and chemically active colloids [18]. RMPCDMD is imple-mented in Fortran 2008 and uses OpenMP for multithreaded operation.…”

Section: Acknowledgementsmentioning

confidence: 99%

“…In this article, we study the L-shaped active colloid (or L motor, for short), explored experimentally by Kümmel et al [3], using Molecular Dynamics simulations. We describe in section 2 the mesoscopic simulation method [18,19], in which the dynamics of both the colloid and the surrounding fluid particles is resolved. We present the bead model for the L shaped colloid in section 3.…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Mesoscopic simulations of anisotropic chemically powered nanomotors

Buyl

2019

Phys. Rev. E

Self Cite

View full text Add to dashboard Cite

Chemically powered self-propelled colloids generate a motor force by converting locally a source of energy into directed motion, a process that has been explored both in experiments and in computational models. The use of active colloids as building blocks for nanotechnology opens the doors to interesting applications, provided we understand the behaviour of these elementary constituents. We build a consistent mesoscopic simulation model for self-propelled colloids of complex shape with the aim of resolving the coupling between their translational and rotational motion. Considering a passive L-shaped colloidal particle, we study its Brownian dynamics and locate its center of hydrodynamics, the tracking point at which translation and rotation decouple. The active L particle displays the same circling trajectories that have been found experimentally, a result which we compare with the Brownian dynamics model. We put forward the role of hydrodynamics by comparing our results with a fluid model in which the particles' velocities are reset randomly. There, the trajectories only display random orientations. We obtain these original simulation results without any parametrization of the algorithm, which makes it a useful method for the preliminary study of active colloids, prior to experimental work. arXiv:1802.03264v2 [cond-mat.soft]

show abstract

Modeling hydrodynamic interactions in soft materials with multiparticle collision dynamics

Howard

Nikoubashman

Palmer

2019

Current Opinion in Chemical Engineering

View full text Add to dashboard Cite

Multiparticle collision dynamics (MPCD) is a flexible and robust mesoscale computational technique for simulating solvent-mediated hydrodynamic interactions in soft materials. Here, we provide a critical overview of the MPCD method and summarize its current strengths and limitations. The capabilities of the method are highlighted by reviewing its recent applications to simulate diverse phenomena, ranging from the flow of complex fluids and thermoosmotic transport to bacterial swimming and active particle self-assembly. We also discuss outstanding challenges and emerging methodological developments that are expected to greatly expand the applicability of MPCD to other systems of technological importance.

show abstract

RMPCDMD: Simulations of Colloids with Coarse-grained Hydrodynamics, Chemical Reactions and External Fields

Cited by 5 publications

References 23 publications

Passive and active colloidal chemotaxis in a microfluidic channel: mesoscopic and stochastic models

Passive and active colloidal chemotaxis in a microfluidic channel: mesoscopic and stochastic models

Mesoscopic simulations of anisotropic chemically powered nanomotors

Modeling hydrodynamic interactions in soft materials with multiparticle collision dynamics

Contact Info

Product

Resources

About