title: A coarse-grained model for DNA-functionalized spherical colloids, revisited: effective pair potential from parallel replica simulations.
abstract: We discuss a coarse-grained model recently proposed by Starr and Sciortino [J. Phys.: Condens. Matter 18, L347 (2006)] for spherical particles functionalized with short single DNA strands. The model incorporates two key aspects of DNA hybridization, i.e., the specificity of binding between DNA bases and the strong directionality of hydrogen bonds. Here, we calculate the effective potential between two DNA-functionalized particles of equal size using a parallel replica protocol. We find that the transition from bonded to unbonded configurations takes place at considerably lower temperatures compared to those that were originally predicted using standard simulations in the canonical ensemble. We put particular focus on DNA-decorations of tetrahedral and octahedral symmetry, as they are promising candidates for the self-assembly into a single-component diamond structure. Increasing colloid size hinders hybridization of the DNA strands, in agreement with experimental findings.
authors: Faculty of Physics, University of Vienna, Boltzmanngasse 5, A-1090 Vienna, Austria. panagiotis.theodorakis@univie.ac.at
authors: Panagiotis E
authors: PE
authors: Theodorakis
authors: Christoph
authors: C
authors: Dellago
authors: Gerhard
authors: G
authors: Kahl
mesh_terms: D001483:Base Sequence; D003102:Colloids / Q000737:chemistry*; D003198:Computer Simulation; D004277:DNA, Single-Stranded / Q000737:chemistry*; D006860:Hydrogen Bonding; D008956:Models, Chemical; D008958:Models, Molecular; D013816:Thermodynamics
chemical_list: D003102:Colloids; D004277:DNA, Single-Stranded