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.
A molecular dynamics (MD) simulation was performed to study the
diffusion of an alkane molecule in siliceous zeolite beta, as a
function of chain length and temperature. The alkane was modeled as a
Lennard-Jones chain, and the simulation was carried out in the
microcanonical ensemble. The results suggest that it is energetically
favorable for the alkane chains to be within close proximity (~2
Å) of the zeolite lattice. However, the histogram data also
show that shorter alkane chains are more likely to be found at farther
distances (~4.5 Å) from the lattice atoms in the zeolite
voids, compared to longer chains that experience more attractive
interactions with the lattice and thus are confined to the small
zeolite cages.
An investigation of the structure of a polyelectrolyte solution
interacting with an attractive wall has been carried out through
molecular dynamics simulations. Total charge density along the polymer
backbone was varied while density profiles and radius of gyration
distributions were measured. Additionally, counterions were
systematically localized to a single surface to study counterion charge
location dependence of polymer position. Increasingly attractive
surfaces result in polymers locating closer to the surface. This
dependence weakens with lesser charge density on polymer. Average
radius of gyration of polyelectrolyte is found to decrease with
increasing charge concentration on backbone, in accordance with known
scaling laws.
Perhaps the most paramount utility of a `toy model' simulation is its
ability to shed light on the fundamental driving forces behind
seemingly complex phenomena such as self-assembly, order-disorder phase
transitions, and the nature of symmetry breaking. Recent experimental
work reported by the Mason group has revealed that the ostensibly
mundane system of hard triangles colliding on a 2-dimensional surface,
in fact exhibits a rich array of order-disorder phase transitions and
intriguingly local chiral symmetry breaking [Zhao, Kun, Robijn
Bruinsma, and Thomas G. Mason.; Nat Commun 3 (May 2012): 801]. Here we
use discrete molecular dynamics to simulate a system of hard regular
triangles undergoing elastic Newtonian collisions on a 2-dimensional
surface. We observe a disorder to order phase transition at packing
fractions above 0.56, and we calculate the mean-squared displacement of
triangles in the liquid-like regime.
Adsorption/repulsion processes of single-atom Lennard-Jones fluid
particles on/by two parallel infinite walls were simulated with Grand
Canonical Monte Carlo method (GCMC). With increased strength
of the particle-wall interactions, more uneven distributions of
particles were observed. However, more even distributions of particles
were observed at elevated temperatures.
Stabilization of (111) polar surface of NaCl crystal by the deposition
of a non-stoichiometric nucleus of Na and Cl atoms has been studied.
Monte Carlo simulations were carried out to study the interaction
between the nucleus and the surface and the potential of mean force
(PMF) was calculated to estimate the equilibrium position of the
nucleus above the surface. Umbrella sampling and Ferrenberg-Swendsen
histogram reweighting technique was applied to calculate the free
energies in the system.
Heterogeneous catalysis and surface reactions are important for many
applications, such as exhaust emission control and synthesis of
chemicals, although their behavior cannot be correctly modeled using
macroscopic rate laws. Python code was developed to simulate the
Ziff-Gulari-Barshad model for surface reactions to help explain why
carbon monoxide oxidation is rapid for some mixtures of carbon monoxide
and oxygen and negligible at others. The model is extremely simple, yet
complex phenomena emerges which helps explain the surface chemistry
which surrounds us. Included in this work is a movie showing how too
much carbon monoxide (relative to oxygen) can lead to the surface being
“poisoned” by stable islands of CO which form on the surface.