[HTML][HTML] The good, the bad and the user in soft matter simulations

J Wong-Ekkabut, M Karttunen - Biochimica et Biophysica Acta (BBA) …, 2016 - Elsevier
Molecular dynamics (MD) simulations have become popular in materials science,
biochemistry, biophysics and several other fields. Improvements in computational resources …

Electrokinetics: insights from simulation on the microscopic scale

B Rotenberg, I Pagonabarraga - Molecular Physics, 2013 - Taylor & Francis
Electrokinetic effects, ie the coupled hydrodynamic and electric phenomena which occur
near charged interfaces, constitute a challenge to theorists due to the variety of length and …

Computational modeling of magnetic particle margination within blood flow through LAMMPS

H Ye, Z Shen, Y Li - Computational Mechanics, 2018 - Springer
We develop a multiscale and multiphysics computational method to investigate the transport
of magnetic particles as drug carriers in blood flow under influence of hydrodynamic …

A parallel fluid–solid coupling model using LAMMPS and Palabos based on the immersed boundary method

J Tan, TR Sinno, SL Diamond - Journal of computational science, 2018 - Elsevier
The study of viscous fluid flow coupled with rigid or deformable solids has many applications
in biological and engineering problems, eg, blood cell transport, drug delivery, and …

Hydrodynamic forces implemented into LAMMPS through a lattice-Boltzmann fluid

FE Mackay, STT Ollila, C Denniston - Computer Physics Communications, 2013 - Elsevier
Long-range hydrodynamic interactions have been implemented into the open-source
molecular dynamics package, LAMMPS, though the creation of a fix, lb_fluid. These …

Implementation of a ternary lattice Boltzmann model in LAMMPS

GRA Kumar, JP Andrews, UD Schiller - Computer Physics Communications, 2024 - Elsevier
The properties of multicomponent fluids are governed by the interplay of phase behavior,
fluid dynamics, and interfacial thermodynamics. A mixture formulation that leverages this …

Enhanced Pulley Effect for Translocation: The Interplay of Electrostatic and Hydrodynamic Forces

N Afrasiabian, M Wei, C Denniston - Biomacromolecules, 2023 - ACS Publications
Solid-state nanopore sensors remain a promising solution to the rising global demand for
genome sequencing. These single-molecule sensing technologies require single-file …

Interplay of deformability and adhesion on localization of elastic micro-particles in blood flow

H Ye, Z Shen, Y Li - Journal of Fluid Mechanics, 2019 - cambridge.org
The margination and adhesion of micro-particles (MPs) have been extensively investigated
separately, due to their important applications in the biomedical field. However, the cascade …

Progress in particle-based multiscale and hybrid methods for flow applications

TR Teschner, L Könözsy, KW Jenkins - Microfluidics and Nanofluidics, 2016 - Springer
This work focuses on the review of particle-based multiscale and hybrid methods that have
surfaced in the field of fluid mechanics over the last 20 years. We consider five established …

Coupling MD particles to a lattice-Boltzmann fluid through the use of conservative forces

FE Mackay, C Denniston - Journal of Computational Physics, 2013 - Elsevier
We propose a new method for coupling both point and composite MD particles to a lattice-
Boltzmann fluid. This coupling is implemented through the use of conservative forces …