Systematic development of coarse-grained polymer models Patrick ...

CHAPTER 1
1.1 Motivation
Introduction
The coupling between polymer models and experiments has improved our understanding of polymer
behavior both in terms of rheology and dynamics of single molecules. Developing these polymer
models is challenging because of the wide range of time and length scales [1, 2]. Mechanical models
of polymers have been used to understand average rheological properties as well as the deviation
a single polymer molecule has from the average response. This leads to more physically significant
constitutive relations, which can be coupled with continuum fluid mechanic simulations to predict
and understand the rheological response of polymer solutions and melts [3].
These models have also been used in conjunction with single molecule polymer experiments [4,
5, 6]. While these have provided insight into the dynamics of polymers in rheological flows, they
have also helped to design single molecule manipulation experiments. Promising research in this
area includes DNA separation and stretching devices.
1.2 General Polymer Physics
A natural place to begin talking about the modeling of polymers is to consider explicitly each of the
atoms. However the bonds between two atoms are quite stiff, with typical frequencies of oscillation
of 10 14 Hz and also small fluctuations away from the average bond length. On the scale of the
entire molecule these small fluctuations will have a minimal impact on the static (configurational)