Structure and Dynamics of Soft Materials in Confined Geometry: Molecular Dynamics Simulation Insight

Soft materials are rich in nature and present in living systems constituting the basic components of living bodies. They are inseparably integrated into the modern world, being critical components in current devices. They undergo large deformations upon presence of small external stimuli due to the conformational and structural fluctuations in constituent molecules near the ambient temperature. The current work probed two classes of soft matter, conjugated polymers confined into nanoparticles, and polymer melts, where entanglements confine the motion of the polymer. The main body of this research focuses on probing the structure, dynamics and internal correlations of rigid luminescent polymers in confined geometry; polydots and their interactions with bio membranes using atomistic molecular dynamics simulations, followed by coarse grained simulations of rheology of entangled branched polymers. The structure, stability and internal correlations of polydots formed by confining luminescent ionizable polymers, poly para phenylene ethynelene (PPEs), into nano dimensions was investigated. Thought the most stable state of these polymers in solutions is extended, in polydots they are trapped in a far from equilibrium state. We find that these polymers remain confined in water independent of the fraction f of ionizable group with majority of the ionizable groups located at the polydot surface, with no correlations between the aromatic rings. The shape and thermal stability are sensitive to both the chain length n and f. These polydots are potential candidates for new class of therapeutic agents and one critical step in the use of any nanoparticle for therapeutics is understanding their interactions with membranes. Here, polydots with different hydrophobicities were introduced into a model bio membrane. The study finds that hydrophobic polydots penetrate the membrane while hydrophilic ones remain adsorbed to the membrane interface. Further we find that polydot surface charge determines the location of polydots with respect to the membrane interface. The last part of the thesis focuses on polymer melts where the effects of polymer topology on the flow properties of the polymers were studied. Using coarse grained simulations, we show that addition of branches reduces the polymer mobility where their length is one major factor. We find that the zero shear viscosity of branched polymer melts increases exponentially. The results are analyzed in terms of the reptation model