Mesoscale Simulation

Mesoscale simulations bridge the gap between atomistic methods (accurate but computationally expensive) and continuum models that treat materials as smooth, featureless media. In coarse-grained molecular dynamics, groups of atoms are represented as single interaction sites, reducing the computational cost enough to simulate systems of millions of particles over microsecond time scales. This is the range where polymer-coated nanoparticles organize into ordered arrays, block copolymers form periodic nanostructures, and hydrogel networks swell and deform, processes directly comparable to what scattering experiments (SAXS) and electron microscopy (TEM) observe.

Nanoparticle self-assembly: Predicting how polymer-coated nanoparticles organize into different crystal structures depending on the number, length, and architecture of the grafted chains

Bottlebrush polymer conjugation: How attaching a branched polymer to a nanoparticle breaks the coating's symmetry and directs particles into two-dimensional ordered patterns

Polymer brush depletion interactions: Measuring the forces that polymer brush layers exert on proteins and particles embedded within them, relevant to biological membrane organization

Hydrogel mechanics: Predicting the stiffness and swelling behavior of polyacrylamide hydrogels using simplified molecular models

We develop and validate coarse-grained models against all-atom simulations and experimental scattering and microscopy data (SAXS, TEM, AFM). These models simulate systems of millions of interaction sites over microsecond timescales.

Yu et al., Advanced Science (2024), Two-regime conformation of grafted polymers

Kim et al., Langmuir (2025), Bottlebrush-driven nanoparticle assembly

Rho et al., ACS Appl. Mater. Interfaces (2025), Hydrogel elasticity via MARTINI

Yu et al., Chemical Physics Reviews (2025), Review: self-assembly of architected macromolecules