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.
In this work, a simplified Lennard-Jones
(LJ) sphere model is used to simulate the aggregation,
adsorption, and structure of interfacial layers of fully hydrophobic,
fully hydrophilic, as well as block (hydrophobic-hydrophilic) polymers.
The structure of the adsorbed polymers at hydrophobic and hydrophilic
surfaces is determined by the equilibrium density profile as a function
of the distance from the surface. Several interesting features of
hydrophobic self assembly are captured, such as the segregation of
hydrophobic moieties, and the ability of hydrophilic groups to
effectively “shield” hydrophobic ones.
Through intramolecular interactions, amino acids largely dictate a
peptide’s structure and flexibility, both of which play
significant roles in a peptide’s binding properties and
function. This model explored the effects of three major residue types
(uncharged hydrophilic, hydrophobic, and charged) on peptide structure
in solution, by utilizing a bead-spring model and the relevant
potentials, including Lennard-Jones and screened Coulomb, to describe
amino acid interactions. As indicated by contact maps and MD movies, MD
simulations of fifteen residue peptides with varied amino acid
configurations captured the relevant structural interactions, such as a
hydrophobic core versus a flexible peptide made up solely of uncharged
hydrophilic residues. Modeling these structuralinteractions can aid the
design of peptides for a specific task, such as fitting in the
catalytic region of an enzyme.
Diblock copolymers are very important in polymer processing because of
their ability to form long range structures. Here a simple model of two
particles denoted A and B are bound togetherby a simple harmonic
potential to form dimers. Both the A-A and B-B interactions are
governed by a standard LJ potential. The A-B interactions are modeled
by a potential consisting of the repulsive part of the LJ interaction
plusa softer, longer ranged (r-4) repulsion. The strength and range of
the additional repulsive interaction is varied by changing a
multiplicative factor λ from 0 to 10. By varying
λ, aggregate structures can be varied from clusters to
chains.
A molecular dynamics (MD) simulation of cerium-doped yttrium aluminum
garnet(YAG:Ce) shows that the excitation characteristics can be modeled
using a Buckingham and truncated Coulomb interaction potential, but
that the emission properties have too high an energy with the potential
functions used here. The MD simulation enables investigation of the
pair distribution function around Ce the optically active dopant in YAG
in the excited state. Such analysis is not currently achievable
experimentally due to the short-lived 4f1 excited state of Ce3+
in YAG:Ce,
which is in the 10’s of nanoseconds.
Molecular dynamics simulations were performed on a system containing
either one or two types of particles confined within a slit pore
geometry. Particle A had a greater
Lennard-Jones
repulsion from the pore walls while particle B
had a greater Lennard-Jones attraction to the wall. The goal was to
understand particle self-diffusion, particle number density
distribution in the pore, and the effect on these properties when
mixing the two particle types with different particle-particle
Lennard-Jones interactions. It was found that the diffusion coefficient
and particle density distribution is quite sensitive to the presence of
other molecular species and its respective interaction potential. These
results have implications towardmolecular design to enhance transport
properties of particles in confinement.
The interaction between AB diblock copolymers with small molecules, C, has been
studied using molecular dynamics. In this experiment, the A molecules are neutral and the
B and C molecules are oppositely charged. The charged molecules aggregate into clusters
with the neutral A blocks surrounding the cluster forming micelles. The mean interparticle
distance, , and equilibration time were measured while varying the size and charge
ratio of the AB copolyelectrolyte.