Coarse graining solvent polymer interactions in bead spring chain models

Long flexible polymers, even in dilute concentrations in a solvent, cause the solution to become non-Newtonian in flow; giving rise to phenomena such as rod climbing, shear thinning, coil-stretch transition etc. A mechanical model of polymer consisting of beads connected by springs has been employed successfully to study the non-Newtonian behavior. In this thesis, we have developed new bead spring models to study flow behavior of long flexible polymers including solvent interactions that was not possible using previous methods. These new models allow us to investigate flow behavior of long polymer molecules like single stranded DNA, vWF protein and synthetic polymers more accurately.;Study of dynamics of polymers in dilute solutions is fundamental for solving various problems involving flow behavior of proteins, DNA and synthetic polymers. In a dilute solution, monomers of a single polymer molecule interacts only with the molecules of the solvent and with other monomers of itself. Therefore, calculating the response of a single polymer molecule in its surroundings is sufficient to predict the bulk properties. Dilute polymer solutions also serve as a simple system in our effort to understand more complex systems—with many polymers and other particles interacting.;As many natural and synthetic polymers are long and the timescale needed to study their rheology are of order of milliseconds to seconds, we seek accurate coarse grained representation of long polymers. One way of coarse graining is to average out the faster motion of solvent molecules in accordance with the fluctuation dissipation theorem, and only consider the slower polymer motion. To do this, a polymer can be represented as beads connected by springs in Brownian dynamics (BD) simulations. It is then important that we accurately model the response of the polymer in the given solvent conditions in these models.;Polymers are usually modeled as random walk chain or worm like chain, which are represented by bead spring chain models. Bead spring chain model works well only for a particular condition known as "theta" condition. To model "real" polymers, an interaction potential between beads was used previously. A large number of such beads with interactions are required to correctly simulate long real polymers. Recent experiments have also shown that real polymers exhibit different behavior than that of ideal chains. Using these experiments and existing theory, we have developed a new bead spring chain model with which we can represent long polymers in different solvent conditions ranging from "good" to "theta" conditions. A simple force balance analysis of a real chain shows that, when we stretch some of these long molecules using elongational flow field, they may not undergo sharp coil to stretch transition as predicted by previous studies. We use BD simulations to confirm our hypothesis. Further, we have found that hysteresis and fluctuations in the coil-stretch transition could be affected by the solvent-polymer interactions.;An effective "solvent quality" arises due to polymer segment repulsions mediated by solvent. The role of attractions between the polymer segments in determining flow behavior is much less understood. Salt ions, nano-particles, proteins etc. can mediate attractions between polymer segments. We model such complex systems by using a bead-spring chain model of polymer interacting with oppositely charged colloids via short-ranged potentials. Using dilute solutions of polymers interacting with colloids, we studied the formation of a compact polymer-colloid structure called a globule, both in equilibrium and in shear. We found that shear flow decreases mean first passage time of polymers and colloids in a random state to form a globule, under some conditions. A globule to stretched state transition of polymers in shear were observed under other conditions. We have also performed preliminary studies using oscillatory flows and semi-dilute solutions of polymers.