(730f) Modeling of DNA-Mediated Pair Interactions Between Nanoparticles
Highly selective and thermally responsive binding of DNA-strands is transferable to nanoparticle systems through covalently tethering these biomolecules onto the particle surfaces. A reliable understanding of how these DNA-functionalized particle (DFP) systems self-assemble requires a deep understanding of inter-particle pair-interactions as a function of molecular-level details of the system such as strand length, the size of the sticky part, the sequence of the DNA-strands and grafting density. In this work, we use a previously developed coarse-grained model  of DNA to construct a temperature dependent inter-particle pair-potential model that is parameterized so as to reflect the molecular description of the DFPs. Umbrella Sampling in combination with Replica-Exchange Molecular Dynamics (REMD) simulations were performed to examine two-particle systems by estimating the potential of mean force (PMF) between nanoparticles at different physical conditions. Eventually, this implicit formulation of the system obtained from a bottom-up approach can efficiently be used to study self-assembly of large DFP systems that would otherwise be computationally infeasible in a simulation with molecular level details.
 Y. Ding, J. Mittal J. Chem. Phys. 141, 184901 (2014).