Date of Award

Spring 1-1-2013

Document Type


Degree Name

Doctor of Philosophy (PhD)


Chemical & Biochemical Engineering

First Advisor

Arthi Jayaraman

Second Advisor

Wounjhang Park

Third Advisor

Christine M. Hrenya

Fourth Advisor

Ivan I. Smalyukh

Fifth Advisor

Mark P. Stoykovich


Precise assembly of nanoparticles is crucial for creating spatially engineered materials that can be used for photonics, photovoltaic, and metamaterials applications. One way to control nanoparticle assembly is by functionalizing the nanoparticle with ligands, such as polymers, DNA, and proteins, that can manipulate the interactions between the nanoparticles in the medium the particles are placed in. This thesis research aims to design ligands to provide a new route to the programmable assembly of nanoparticles.

We first investigate using Monte Carlo simulation the effect of copolymer ligands on nanoparticle assembly. We first study a single nanoparticle grafted with many copolymer chains to understand how monomer sequence (e.g. alternating ABAB, or diblock AxBx) and chemistry of the copolymers affect the grafted chain conformation at various particle diameters, grafting densities, copolymer chain lengths, and monomer-monomer interactions in an implicit small molecule solvent. We find that the size of the grafted chain varies non-monotonically with increasing blockiness of the monomer sequence for a small particle diameter. From this first study, we selected the two sequences with the most different chain conformations--alternating and diblock--and studied the effect of the sequence and a range of monomer chemistries of the copolymer on the characteristics of assembly of multiple copolymer-functionalized nanoparticles. We find that the alternating sequence produces nanoclusters that are relatively isotropic, whereas diblock sequence tends to form anisotropic structures that are smaller and more compact when the block closer to the surface is attractive and larger loosely held together clusters when the outer block is attractive.

Next, we conduct molecular dynamics simulations to study the effect of DNA ligands on nanoparticle assembly. Specifically we investigate the effect of grafted DNA strand composition (e.g. G/C content, placement and sequence) and bidispersity in DNA strand lengths on the thermodynamics and structure of assembly of functionalized nanoparticles. We find that higher G/C content increases cluster dissociation temperature for smaller particles. Placement of G/C block inward along the strand decreases number of neighbors within the assembled cluster. Finally, increased bidispersity in DNA strand lengths leads a distribution of inter-particle distances in the assembled cluster.