LAMMPS-a flexible simulation tool for particle-based materials modeling at the atomic, meso, and continuum scales

AP Thompson, HM Aktulga, R Berger… - Computer Physics …, 2022 - Elsevier
Since the classical molecular dynamics simulator LAMMPS was released as an open source
code in 2004, it has become a widely-used tool for particle-based modeling of materials at …

High‐Throughput Generation of 3D Graphene Metamaterials and Property Quantification Using Machine Learning

Z Yang, MJ Buehler - Small Methods, 2022 - Wiley Online Library
Abstract 3D graphene assemblies are proposed as solutions to meet the goal toward
efficient utilization of 2D graphene sheets, showing excellent performances in applications …

Diffusion coefficients and MSD measurements on curved membranes and porous media

A Ledesma-Durán, LH Juárez-Valencia - The European Physical Journal …, 2023 - Springer
We study some geometric aspects that influence the transport properties of particles that
diffuse on curved surfaces. We compare different approaches to surface diffusion based on …

Effect of confinement and topology: 2-TIPS vs. MIPS

N Venkatareddy, J Mandal, PK Maiti - Soft Matter, 2023 - pubs.rsc.org
2-TIPS (two temperature induced phase separation) refers to the phase separation
phenomenon observed in mixtures of active and passive particles which are modelled using …

Curvature-controlled geometrical lensing behavior in self-propelled colloidal particle systems

PWA Schönhöfer, SC Glotzer - Soft Matter, 2022 - pubs.rsc.org
In many biological systems, the curvature of the surfaces cells live on influences their
collective properties. Curvature should likewise influence the behavior of active colloidal …

Probing the interplay between dendritic spine morphology and membrane-bound diffusion

M Adrian, R Kusters, C Storm, CC Hoogenraad… - Biophysical journal, 2017 - cell.com
Dendritic spines are protrusions along neuronal dendrites that harbor the majority of
excitatory postsynapses. Their distinct morphology, often featuring a bulbous head and …

Energetically favoured defects in dense packings of particles on spherical surfaces

S Paquay, H Kusumaatmaja, DJ Wales, R Zandi… - Soft Matter, 2016 - pubs.rsc.org
The dense packing of interacting particles on spheres has proved to be a useful model for
virus capsids and colloidosomes. Indeed, icosahedral symmetry observed in virus capsids …

Microparticle assembly pathways on lipid membranes

C van der Wel, D Heinrich, DJ Kraft - Biophysical Journal, 2017 - cell.com
Understanding interactions between microparticles and lipid membranes is of increasing
importance, especially for unraveling the influence of microplastics on our health and …

Lipid membranes supported by polydimethylsiloxane substrates with designed geometry

M Rinaldin, SLD Ten Haaf, EJ Vegter, C van der Wel… - Soft Matter, 2024 - pubs.rsc.org
The membrane curvature of cells and intracellular compartments continuously adapts to
enable cells to perform vital functions, from cell division to signal trafficking. Understanding …

Diffusion, density, and defects on spheres

JE Bond, AJ Yeh, JR Edison, MA Bevan - Soft Matter, 2024 - pubs.rsc.org
We simulate and model diffusion of spherical colloids of radius, a, on spherical surfaces of
radius, R, as a function of relative size and surface concentration. Using Brownian dynamics …