  DNA-functionalized particles have great potential for the design of complex
self-assembled materials. The major hurdle in realizing crystal structures from
DNA-functionalized particles is expected to be kinetic barriers that trap the
system in metastable amorphous states. Therefore, it is vital to explore the
molecular details of particle assembly processes in order to understand the
underlying mechanisms. Molecular simulations based on coarse-grained models can
provide a convenient route to explore these details. Most of the currently
available coarse-grained models of DNA-functionalized particles ignore key
chemical and structural details of DNA behavior. These models therefore are
limited in scope for studying experimental phenomena. In this paper, we present
a new coarse-grained model of DNA-functionalized particles which incorporates
some of the desired features of DNA behavior. The coarse-grained DNA model used
here provides explicit DNA representation (at the nucleotide level) and
complementary interactions between Watson-Crick base pairs, which lead to the
formation of single-stranded hairpin and double-stranded DNA. Aggregation
between multiple complementary strands is also prevented in our model. We study
interactions between two DNA- functionalized particles as a function of DNA
grafting density, lengths of the hybridizing and non-hybridizing parts of DNA,
and temperature. The calculated free energies as a function of pair distance
between particles qualitatively resemble experimental measurements of
DNA-mediated pair interactions.
