Application of molecular modeling to polymer grafted nanostructures

Polymer chains undergo conformational transitions in response to a change in solvent quality of their environment, making them strong candidates to be used in smart nanometer-scale devices. In the present work molecular modeling is used to explore grafted polymer structures with various functionalities. The first part of this research focuses on two examples of selective transport through nanopores modified with polymer brush structures. The first is the investigation of solvent flow through nanopores grafted with linear chains. Molecular dynamics (MD) simulations are used to demonstrate how a stretch-collapse transition in grafted polymer chains can be used to control solvent flow rate through a nanopore in response to environmental stimuli. A continuum fluid dynamics method based on porous layer model for describing flow through the smart nanopore is described and its accuracy is analyzed by comparing with the results from MD simulations. The continuum method is then applied to determine regulation of water permeation in response to pH through a poly(L-glutamic acid) grafted nanoporous membrane. A second example is use of a rod-coil transition in “bottle brush” molecules that are grafted to the inside of a nanopore to size select macromolecules as they diffuse through the functionalized nanopores. These stimuli-responsive nanopores have a variety of potential applications including molecular sorting, smart drug delivery, and ultrafiltration, as well as controlled chemical release.; Tethered polymers play an important role in biological structures as well. In the second part of the research, application of atomistic simulations to characterize the effect of phosphorylation on neurofilament structure is presented. Neurofilaments are intermediate filaments that regulate axonal diameter through their long, flexible side arms extending from the central core. Their functionality is imparted by polymer brush like structure that causes steric repulsion between the filaments. A disruption in their structure/distribution is a hallmark of several neuromuscular diseases including amyotrophic lateral sclerosis (ALS). Further, there is evidence that phosphorylation alters the structure of side arms, which is thought to be associated with ALS. MD simulations are performed to characterize the structure of neurofilament side arms as a function of phosphorylation. The simulations indicate that phosphorylation significantly alters the side arm size, which may affect the axonal caliber. The results may also shed light on the mechanism of ALS.