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 Monte Carlo (MC) simulation is performed to study the effect of the dipole-dipole repulsion
interaction to the size of Lennard-Jones (LJ) particle aggregation as an analogy of Liquid condensed (LC)
domain formation of Zwitterionic surfactant, which contains the dipole moment, but neutral ,at the air-
water interface. The result shows the similar qualitative tendencies of changing characteristic
aggregation size with the ratio of dipole-dipole repulsion to L-J potential, compared to the result from
the simple calculation of the free energy to find the size of LC domains at equilibrium. In addition, we
find that temperature effect on the aggregation size of particles with this potential is also well agreed
with experimental observation.
In order to estimate the absolute perpendicular growth rate of a crystal surface, we need to
estimate the free energy barrier for the incorporation and removal of growth units. In this work,
an all-atom molecular dynamics with biased umbrella sampling and WHAM was used to
calculate the potential of mean force (PMF) as a function of the perpendicular distance between
the growth unit and the surface of one of the crystal faces of alpha-glycine. From the PMF curve,
the surface incorporation/disincorporation energy (binding energy) was estimated.
Glucagon and insulin play major roles in regulating blood glucose levels, and people with type 1
diabetes mellitus need exogenous sources of these hormones for survival. One major issue faced
by glucagon pumps that automate these exogenous injections is the problem of stability, as
glucagon rapidly forms precipitates upon standard clinical preparation which greatly decrease
their shelf lives. To understand general trends that cause these effects and determine conditions
under which glucagon can be stored in an aqueous solution, a molecular dynamics simulation
was conducted to illustrate the properties of a glucagon molecule under varying pH and
temperature conditions. Glucagon was modeled as a bead-string polymer of 29 coarse-grain units,
with each unit representing a separate amino acid and thus having its individual parameters,
including different radii and charge. The changes in pH was modeled as changes in the total
charge of each amino acid unit based on the charge of its R-group(s), and an Anderson
thermostat was utilized to model changes in temperature. The radius of gyration of the simulated
glucagon molecule increases with the distance from neutral pH. A similar, but plateauing trend
can be seen with increasing simulation temperature. These trends have comparable counterparts
to experimental results found in literature.
Vapor-liquid coexistence properties are studied using a Gibbs ensemble Monte Carlo simulation. Two
simulation boxes with a fixed total number of Argon atoms and a constant total volume are coupled to
each other (i.e., the two boxes can exchange volumes and particles), so that the phase coexistence
between liquid and vapor can be achieved. Then, a series of simulations were run varying the reduced
temperature. The simulation results (phase diagram) and the literature values are reasonably matched.
The more realistic and complete model of a potential to describe interactions between particles may
improve the quality of a simulation result in the future.
The anomalous properties of water give rise to many interesting natural phenomena such
as the hydrophobic interaction. By understanding the mathematical models behind certain
physical interactions, one can predict how similar systems may behave in the real world.
One of these interactions, the free energy of solvation, is of interest. In order to find
the Helmholtz free energy of solvation of a methane-like molecule in water solvent
(spherically symmetric water molecules), Monte Carlo simulation is used. Water-water
interactions are modeled by the Lennard-Jones plus Gaussian (LJG) interaction while the water-methane
interaction is governed by a simple Lennard-Jones. These models in conjunction with the
Widom test particle insertion method are used.
The settling and packing properties of colloidal suspensions of large hard spheres in an effective
gravitational field are investigated by a Monte Carlo constant-NVT simulation. The ratio of an
effective gravitational potential to the repulsion/attraction potential in the hard sphere (G/e) is a
critical parameter that determines the surface coverage and packing properties of the system.
The surface coverage, phi, as well as the radial distribution function (RDF), g(r), are calculated at
a hard wall for varying suspension volume fractions. Attractive hard spheres (e < 0)
agglomerate before sedimentation, causing phi to be decreased.