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.
Water is the universal solvent of life, crucial to the function of all biomolecules. Proteins,
membranes, and nucleic acids all have particular structural properties that are driven by the presence of
water. The “hydration shell” of three to four water molecules at biological surfaces is thought to be
especially relevant for lubricating dynamic interactions, such as the binding of proteins.
Here we explore the phenomenon of hydration dynamics—the local diffusion of water near a simplified surface.
This is accomplished by a molecular dynamics simulation to measure two-dimensional diffusion
coefficients for water molecules bounded by hydrophobic walls. We use an optimized coarse-grained
spherical-symmetric model to describe water-water interactions, the Lennard Jones plus Gaussian (LJG)
pair potential, and a 9-3 Lennard-Jones potential to treat the hydrophobic barriers as solid walls in
contact with a hard sphere fluid. We find a increase of the self-diffusivity D for molecules close to the
hydrophobic barriers, and an overall increase in water diffusion between the hydrophobic plates relative
to the bulk case.
Polyelectrolyte bridging occurs in systems of macroions with oppositely charged polyelectrolytes.
Attractive forces between the like-charged macroions are induced by the polyelectrolytes, which can
adsorb to two macrions and form a “bridge” between them. These interactions are important in many
biological systems (Podgornik 2006). In this study, two positively charged macroions and one negatively
charged polyelectrolyte were modeled to explore the fundamentals of polyelectrolyte bridging. The model
used was able to produce bridging phenomena. Shorter polyelectrolyte chains were able to induce a
greater attractive force at small macroion separations, but longer chains were able to maintain the force at
larger macroion separations.
A set of molecular dynamics simulations of a charged/neutral peptide between charged walls are
performed. The distributions of end-to-end distances and radius of gyration show the differences in
conformations between a charged peptide and a neutral peptide. The free energy coming from the charged
walls is computed as a function of the distance between two walls using WHAM.
Simulations were carried out to investigate phase segregation of insoluble alloy nanoparticles
(NPs) such as PtAg. The distributions of Pt and Ag within a ~24 Å (231 atom) cluster were
varied using the Monte Carlo method with effective medium theory potentials to model atomic
interactions at 1073 K. The radial distribution functions and radial atom fraction profiles for Pt
and Ag atoms showed that Ag prefers to segregate onto the PtAg nanoparticle surface for Ag
compositions between 5-50 atom%. The presence of surface Ag at a majority of highly
unsaturated octahedral edge sites would have a profound effect on catalytic selectivity,
particularly at high temperatures. These findings are in agreement with previous
characterization and catalytic testing of Pt91Ag7 octahedral nanoparticles for partial C2H2
hydrogenation.
A three dimensional molecular dynamics simulation was performed for a simple Lennard-Jones
system to study a liquid-vapor interface. A clear separation can be seen between the two phases and
with the density of the liquid and gas being approximately 5 and 0.8, respectively, in reduced units.
During the production run the location of the liquid on the z-axis was not entirely stable, which may
imply that the system hasn’t completely reached equilibrium at the start of the production run or that
more particles are needed to obtain good statistics.
Mass transport in porous medium is highly dependent on the pore size,
shape, and tortuosity, which have been interesting factors on porous
materials. The effect of pore geometry (pore shapes and tortuosity)
on oxygen diffusivity was studied by using NVT molecular dynamic simulations
with 6-12 Lennard-Jones potential. In the implicitly built slit-like pore
walls, oxygen diffusion was appeared to be strongly affected by pore
geometry.