Gallery of final projects
Students in the course designed and performed simulations
of coarse-grained models for a variety of systems of interest to them.
As a part of their projects, students developed movies of
simulation trajectories to visualize their results. The
titles below are links to the report for each project, and a link is
also provided to the source code.
Polymer solutions are presently used in many important industrial applications, including coatings,
commodity materials, microelectronics, pharmaceuticals and medical devices, in addition to a plethora
of research applications. In these applications the transport properties of the polymer and solvent are
of great importance. The goal of this work was to use constant-NVE molecular dynamics simulation to
investigate the diffusion properties of a simplified polymer-solvent system composed of linear Lennard-
Jones polymer molecules and solvent molecules over a range of molecular sizes and polymer
concentrations. The results suggest that in this system polymer diffusivity decreases linearly with
increasing polymer concentration for a range of polymer lengths. Additionally, polymer diffusivity obeys
a power law relationship with polymer length however the strength of the power law relationship
increases with increasing polymer concentration. Solvent diffusivity appears to decrease linearly with
increasing polymer concentration and displays a weak power law relationship with polymer length,
although this power law relationship becomes more apparent at high polymer concentrations.
Polymers that are end-grafted to a substrate, as known as a polymer brushes, are
commonly used to modify surface properties. Polymer brush systems have many practical
applications including as a way to create low-friction surfaces. This remarkable property can be
observed using simple coarse-graining models in computational efforts. Molecular dynamics
simulations of a polymer brush system were conducted and the friction coefficient was
subsequently calculated. The movie shows two surfaces functionalized with polymer brushes
that are brought in contact before a shear velocity is applied to the upper wall.
Availability of experimental data now provides a basis for developing computer
models to investigate mechanical events in biological systems. Herein, a coarse-grained model
that attempts to remove all unnecessary degrees of freedom, while accurately predicting the
entropic elasticity of DNA is presented. The model was evaluated with molecular dynamics
simulations of super-coiled DNA uncoiling. In particular, the relative end-to-end extension (z/L)
as a function of applied force was calculated. Comparison of model predictions with
experimental data suggests that the coarse-graining employed represents a starting point for
developing more useful models, in that relative DNA extension was accurately predicted for the
low force limit while at higher forces the model failed.
A Molecular Dynamics simulation is developed to measure the dilatational (compression) rheological
properties of a fluid and is demonstrated with the Lennard-Jones 12-6 atomic fluid. Small amplitude, oscillatory volume
changes imposed on the fluid result in anoscillatory pressure response, from which the complex dilatational modulus is
computed. A frequency sweep at low strain amplitude shows that the LJ fluid is elastic dominant with an elastic
compression modulus that compares well to the values obtained from equilibrium pressure-density isotherms, computed
here and in literature.