We are investigating the impact of confinement on the morphology of semi-flexible polymer chains. Unlike most previous polymer studies, this work incorporates computationally demanding orientation interactions within the system through a worm-like chain model. These orientation effects are needed to correctly model systems such as liquid crystals and biological macromolecules. In particular, DNA and viral structures within cells can be modeled with this approach.
Through the addition of orientations, we can model polymer systems with a range of stiffnesses – from highly flexible, long chain polymers to the short and rigid polymer rods comonly seen in biological systems, and anything in between.
The high computational cost of this orientation model requires new computational approaches. Utilizing the power of high performance computing and a highly scalable finite element approach incorporating several advanced methodologies, we use self-consistent field theory to calculate the structure adopted by chains within confined geometries analogous to cells or droplets.
The self consistant field model searches for a stationary structual configuration resulting in a minimum energy polymer microstructure. Our implementation follows a standard method, however, our use of finite elements allows us to easily tackle arbitrary shapes which the commonly used spectral methods cannot. Insight from this work will be useful for better understanding a wide range of semi-flexible macromolecules.