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.
Both repulsive and attractive terms are necessary in the microscopic
pair potential in order to observe macroscopic liquid and vapor
phases. We explore the conditions for phase equilibria for particles
interacting via Lennard-Jones and square-well pair potentials. A wide
range of particle densities are simulated in the grand canonical Monte
Carlo ensemble using the Wang-Landau method to develop a histogram
flat for all particle numbers. We find that the critical temperature
for a square-well fluid scales with the range of the attractive energy
between particles. In particular, when the attractive range is half
the width of the hard-shell diameter (lambda = 1.5) the temperature-density
phase envelope is similar to that for the Lennard-Jones fluid.
The behavior of polymer chains both in melt and solution is strongly
affected by forces that act to disrupt the ideal distribution of
conformations accessible to the chains. As polymers approach a hard wall,
they continuously experience an increasing entropic repulsion long before
packing or hard-core effects lead to a divergence in the interaction
energy. Even with a purely repulsive wall interaction, adsorption behavior
is observed for high temperature and fluid density. As the fluid is cooled
the adsorption behavior evidently vanishes and a simple monotonic depletion
layer is recovered. Umbrella sampling was employed to calculate the
potential of mean force along the axis perpendicular to the plane of the
hard wall, ensuring sufficient sampling in regions adjacent to the wall.
The dynamic development of a gas enrichment layer along a hydrophobic interface was studied
using a Molecular Dynamics (MD) simulation of a simple 3-component Lennard-Jones (LJ) fluid system.
The simulation consisted of a wall modeled by a single sheet of explicit LJ atoms held fixed via a
harmonic potential and maintained at constant temperature using an Andersen thermostat. A liquid film
with gas dissolved in it was placed next to the wall, and the parameters were tuned initially such that
the interface is hydrophilic (i.e. the interaction between the liquid and wall atoms is more favorable
than the interaction between wall and gas atoms). After equilibration, the wall/particle interaction
parameters were switched from being hydrophilic to hydrophobic, and the gas deposition process was
observed until the enrichment layer became fully developed. A movie of one of the trajectories was
rendered in Chimera, and an animation of the evolution of the liquid/gas density profiles in the system
was prepared by averaging over 10 independent MD trajectories. The initial and final (equilibrium)
states of this process show excellent agreement with literature
Alkanethiol Self-Assembled Monolayers (SAMs) are a class of spontaneously adsorbing
molecules—containing an adsorbing thiol head group and a (possibly end-functionalized)
hydrocarbon tail—that are widely used to form dense, uniform, and sometimes
functionalized monolayers in the surface science community. In this study, the effect of
the hydrophobic tail length on the adsorption of alkanethiols onto gold surfaces was
examinedusing Molecular Dynamics simulations. Head group and tail group density
profiles—as functions of distance from the gold surface—were monitored during the
simulations to show the time evolution of the monolayer adsorption. This study found
that increasing the SAM hydrophobic tail length increased the hydrophobic interactions
between the tail groups, and impeded head group adsorption.
Organic photovoltaic materials employ conjugated polymers and fullerene-based
molecules to absorb photons and transport captured charges. The phase separation during
processing in these systems is critical for their efficiency. To that end, phase separation
and dynamics of polythiophene (M= 2, 4, 10, 20, 40,60), fullerene mixtures are
investigated using (NVE) molecular dynamics with a Lennard-Jones chain force-field.
Radial distribution functions show a slight increase in fullerene packing after system has
been annealed at T=1.5 dimensionless temperature, in agreement with experimental data.
Polythiophene diffusion constants follow a power law relationship based on polymer
length.
A dilute system of equally sized anionic polysaccharides suspended in an implicit water
solvent was studied using molecular dynamics. The radial distribution functions were generated
for these systems as a function of the polysaccharide chain length (M) and electrostatic strength
(?). These simulations indicate that for anionic polysaccharides of equal charge, molecular
aggregation or clustering in water is favored as the polysaccharide chain length increases.