Multiscale modeling for complex macromolecular systems: Methodologies and applications

The objective of this dissertation is to understand the binding mechanism between flexible macromolecules and guest species in solution using multiscale molecular modeling strategies, including: ab initio electronic structure theory, all-atom classical molecular dynamics simulations, coarse-grained molecular dynamics simulations, and statistical eld theory. A brief summary of the subsequent chapters in this thesis is provided. Chapters 2 - 7 and Appendix A are self-contained units complete with literature review and bibliography

Existence and emergent dynamics of quadratically separable states to the Lohe tensor model

A tensor is a multi-dimensional array of complex numbers, and the Lohe tensor model is an aggregation model on the space of tensors with the same rank and size. It incorporates previously well-studied aggregation models on the space of low-rank tensors such as the Kuramoto model, Lohe sphere and matrix models as special cases. Due to its structural complexities in cubic interactions for the Lohe tensor model, explicit construction of solutions with specific structures looks daunting. Recently, we obtained completely separable states by associating rank-1 tensors. In this paper, we further investigate another type of solutions, namely "{\it quadratically separable states}" consisting of tensor products of matrices and their component rank-2 tensors are solutions to the double matrix model whose emergent dynamics can be studied using the same methodology of the Lohe matrix model

Multiscale Modeling for Host-Guest Chemistry of Dendrimers in Solution

Dendrimers have been widely used as nanostructured carriers for guest species in a variety of applications in medicine, catalysis, and environmental remediation. Theory and simulation methods are an important complement to experimental approaches that are designed to develop a fundamental understanding about how dendrimers interact with guest molecules. This review focuses on computational studies aimed at providing a better understanding of the relevant physicochemical parameters at play in the binding and release mechanisms between polyamidoamine (PAMAM) dendrimers and guest species. We highlight recent contributions that model supramolecular dendrimer-guest complexes over the temporal and spatial scales spanned by simulation methods ranging from all-atom molecular dynamics to statistical field theory. The role of solvent effects on dendrimer-guest interactions and the importance of relating model parameters across multiple scales is discussed

Reintroducing explicit solvent to a solvent-free coarse-grained model

A unique coarse-grained modeling scheme that combines a systematic, solvent-free multiscale coarse-graining algorithm for a complex macromolecule with an existing coarse-grained solvent model is proposed. We show that this procedure efficiently and reliably describes the interactions for complex macromolecules, using the specific example of dendrimers binding phenanthrenes in water. The experimentally measured binding capacity is predicted by the unique coarse-grained modeling approach; the conditions for this simulation are beyond what could be reasonably simulated with an all-atom molecular dynamics simulation