Date of Award

Spring 2017

Project Type

Thesis

Program or Major

Chemical Engineering

Degree Name

Master of Science

First Advisor

Harish Vashisth

Second Advisor

Russell T Carr

Third Advisor

Kang Wu

Abstract

We have explored the conformational dynamics of the peptide-appended pillar[5]arene (PAP) channel in lipid and block copolymer (BCP) membranes through the use of molecular dynamics (MD) simulations. The novel polymeric structures trans-1,4-polybutadiene (PB), trans-1,4-polyisoprene (PI), and poly-2-methyl-2-oxazoline (PMOXA) were created and parameterized. These structures were then used to build and simulate pure PB12PEO9, PB23 PEO16 , PI12 PEO9 , and PI23PEO16 synthetic BCP membranes. In addition, simulations of the PAP channel inserted into lipid (POPC), PB12 PEO9 , and PB23PEO16 membranes were conducted. Results of simulations containing PAP suggest that the membrane environment can affect the channel dynamics and potentially its diffusive as well as transport characteristics. Next, we began to explore the microscopic structure of block copolymer membranes using coarse-grained methods. We tested original MARTINI force-field parameters by simulating the self-assembly of a POPC lipid bilayer. We then used the MARTINI force-field to build and simulate coarse-grained models of PB12PEO9. The original MARTINI force-field was unable to show the self-assembly of PB 12PEO9 and must therefore be further optimized to observe the desired behavior.

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