Molecular dynamics of dilute solutions of polymers and DNA with applications.

摘要

This thesis aims to bridge the macroscopic properties and microscopic behavior of macromolecules in flows. We use Brownian dynamics simulations with the multi-beadspring model without adjustable parameters to predict the behavior in flow of DNA, and conventional polymer molecules, such as polystyrene, and compare the predictions with experimental measurements in extensional and shearing flows. Using parameters obtained a priori from molecular theories and molecular characteristics, we are able to quantitatively or semi-quantitatively predict both the equilibrium and transient deformation properties of individual DNA and other polymer molecules in flowing solutions. From the predictions of molecular deformation in flows, we are able to explain the macroscopic rheological properties of these solutions. The simulations indicate that molecules go through a variety of different conformations (such as Coil, Kink, Fold, Dumbbell, Half-Dumbbell) that affect molecular contributions to the macroscopic properties, such as stress or viscosity, in flows.; With this success in predicting molecular deformations in bulk flows, we then study polymer flow behavior near a solid surface in both simple steady shearing flow and in the flow generated by an evaporating droplet, the latter flow being used in the optical mapping of DNA. The experimental results for DNA molecules in an evaporating droplet indicate that faster evaporation results in better stretching and more taut molecular conformations in the final stage of drying. These results show excellent agreement with the predictions of Brownian dynamics simulations performed by Manish Chopra, a student in our group. The results will be helpful in designing flows for genetic analysis.; Overall, this work can lead to improving understanding of molecular behavior in flows, and such progress will not only benefit the conventional polymer industries, but also emerging technologies, such as high-throughput DNA micro-array analysis.