CONFORMATIONAL PROPERTIES AND ENTROPIC PARTITIONING OF TOPOLOGICALLY COMPLEX POLYMERS UNDER CONFINEMENT - Final Report

The effect of molecular topology (e.g., branch and loop structures) on the solution properties of polymers is subtle and not well characterized. Because the conformational entropy of a polymer depends on its topology, many properties are affected by it such as its size and shape, mobility, bulk-to-pore partitioning, adsorption strength on surfaces, and depletion-induced forces on colloidal surfaces. We have systematically studied the effect of molecular topology on the structure and entropic partitioning of linear, branched, hyper-branched, cyclic, and hyper-cyclic polymers in a bulk solution and in pores. Ours is the first simulation study aimed at characterizing the conformational properties of hyper-cyclic molecules. Key findings: Our results show how differences in molecular architecture can be used to partition polymers in a porous media e.g., a highly branched polymer tends to be depleted in narrow pores (smaller than the coil size) relative to a less branched chain of equal molecular weight, but this trend is reversed in wide pores. It was also found that intra-molecular crosslinking (associated with cyclic structures) is an effective way to tune the conformational entropy of a polymer; the more crosslinks a molecule has, the smaller its conformational entropy, and the easier it is to adsorb it onto attractive pore walls. Intra-crosslinked chains are thus more effective steric stabilizer of colloid particles than linear chains (which are better depleting agents). Simulations were also used to investigate the mechanism of entropic trapping for model linear and branched DNA molecules as they go from a deep channel to a shallow channel driven by an electric field. In such a system, a molecule whose radius of gyration is larger than the gap of the shallow channel tends to get temporarily trapped at its entrance. Our results show that at moderate and strong fields, longer chains escape faster than shorter ones because, in the absence of significant differences in the free energy barrier for escape, larger chains access a larger entrance area to the narrow channel; these results are in agreement with reported experimental observations