Molecular modeling and simulation for proteins and polymer membranes

A computational framework was used to expand the applicable length and time scale of molecular dynamics simulations (MD) by developing a multiscale CG parameterization approach for biomolecules, and an investigation on the adsorption mechanism of an endocrine disrupting compound onto polymer membran...

Full description

Saved in:
Bibliographic Details
Main Author: Christian, Bope Domilongo
Other Authors: Zhang Zuoqi
Format: Theses and Dissertations
Language:English
Published: 2017
Subjects:
Online Access:http://hdl.handle.net/10356/72871
Tags: Add Tag
No Tags, Be the first to tag this record!
Institution: Nanyang Technological University
Language: English
id sg-ntu-dr.10356-72871
record_format dspace
spelling sg-ntu-dr.10356-728712023-02-28T18:32:13Z Molecular modeling and simulation for proteins and polymer membranes Christian, Bope Domilongo Zhang Zuoqi Cheng Yu Lu Lanyuan School of Biological Sciences DRNTU::Science::Biological sciences::Biochemistry A computational framework was used to expand the applicable length and time scale of molecular dynamics simulations (MD) by developing a multiscale CG parameterization approach for biomolecules, and an investigation on the adsorption mechanism of an endocrine disrupting compound onto polymer membranes. For a multiscale model to parameterize CG-ENM force fields and structure-based model, we developed an improve fluctuation matching method, which is based on the relative entropy method, pioneered by Shell and colleagues. This method includes a non-negativity constraint and Newton Raphson’s algorithm for iteration. Furthermore, this framework incorporates pairwise force constant correlations, which play an important role in the study of protein dynamics. Similar to the well-established fluctuation matching proposed by Lyman and coworkers, our heterogeneous ENM parameterization using the relative entropy method with non-negativity constraints, including a pairwise force constant correlation which plays an important role in the study of protein dynamics. Furthermore, fluctuation matching based on relative entropy method guarantees global optimum, with fast convergence. For the adsorption of 17-α ethinylestradiol (EE2), we investigate the adsorption mechanism of EE2 from wastewater using MD simulations of monomers and polymer membranes level to validate experimentally observed results. Our findings from monomers level simulations with the small molecules EE2, and testosterone (polyether sulfone-EE2, polysulfone-EE2, polyvinylidene fluoride-EE2, polyether sulfone-testosterone) and their analogous structures as well as polymer membranes simulations with the small molecules EE2 and testosterone (polyether sulfone-EE2 polyvinylidene fluoride-EE2 and polyether sulfone-testosterone) shows that the enhancement of binding affinity between PES and EE2 from both simulation set ups (monomer level and polymer membranes level) obtained from binding free energy, mean-squared displacement, diffusion coefficients, and insight atomistic interaction are attributed mainly to the π-π interaction and hydrogen bond. Our simulation findings are in agreement with the experimental results. Furthermore, to verify prediction veracity of our computational framework, additional systems are considered such as polyamide 612 at monomer and polymer membrane level and polystyrene membrane. In total, the binding free energies of all the systems considered in this study are in the order as; PES-EE2 > PES-testosterone > PS-EE2> PA612-EE2 > PVDF-EE2 > PVDF-testosterone. To the best of our knowledge, these results suggest that the microporous PES hollow fiber membrane system is the most cost-effective approach that can effectively and efficiently remove EE2 at low concentrations. ​Doctor of Philosophy (SBS) 2017-12-08T09:55:30Z 2017-12-08T09:55:30Z 2017 Thesis Christian, B. D. (2017). Molecular modeling and simulation for proteins and polymer membranes. Doctoral thesis, Nanyang Technological University, Singapore. http://hdl.handle.net/10356/72871 10.32657/10356/72871 en 160 p. application/pdf
institution Nanyang Technological University
building NTU Library
continent Asia
country Singapore
Singapore
content_provider NTU Library
collection DR-NTU
language English
topic DRNTU::Science::Biological sciences::Biochemistry
spellingShingle DRNTU::Science::Biological sciences::Biochemistry
Christian, Bope Domilongo
Molecular modeling and simulation for proteins and polymer membranes
description A computational framework was used to expand the applicable length and time scale of molecular dynamics simulations (MD) by developing a multiscale CG parameterization approach for biomolecules, and an investigation on the adsorption mechanism of an endocrine disrupting compound onto polymer membranes. For a multiscale model to parameterize CG-ENM force fields and structure-based model, we developed an improve fluctuation matching method, which is based on the relative entropy method, pioneered by Shell and colleagues. This method includes a non-negativity constraint and Newton Raphson’s algorithm for iteration. Furthermore, this framework incorporates pairwise force constant correlations, which play an important role in the study of protein dynamics. Similar to the well-established fluctuation matching proposed by Lyman and coworkers, our heterogeneous ENM parameterization using the relative entropy method with non-negativity constraints, including a pairwise force constant correlation which plays an important role in the study of protein dynamics. Furthermore, fluctuation matching based on relative entropy method guarantees global optimum, with fast convergence. For the adsorption of 17-α ethinylestradiol (EE2), we investigate the adsorption mechanism of EE2 from wastewater using MD simulations of monomers and polymer membranes level to validate experimentally observed results. Our findings from monomers level simulations with the small molecules EE2, and testosterone (polyether sulfone-EE2, polysulfone-EE2, polyvinylidene fluoride-EE2, polyether sulfone-testosterone) and their analogous structures as well as polymer membranes simulations with the small molecules EE2 and testosterone (polyether sulfone-EE2 polyvinylidene fluoride-EE2 and polyether sulfone-testosterone) shows that the enhancement of binding affinity between PES and EE2 from both simulation set ups (monomer level and polymer membranes level) obtained from binding free energy, mean-squared displacement, diffusion coefficients, and insight atomistic interaction are attributed mainly to the π-π interaction and hydrogen bond. Our simulation findings are in agreement with the experimental results. Furthermore, to verify prediction veracity of our computational framework, additional systems are considered such as polyamide 612 at monomer and polymer membrane level and polystyrene membrane. In total, the binding free energies of all the systems considered in this study are in the order as; PES-EE2 > PES-testosterone > PS-EE2> PA612-EE2 > PVDF-EE2 > PVDF-testosterone. To the best of our knowledge, these results suggest that the microporous PES hollow fiber membrane system is the most cost-effective approach that can effectively and efficiently remove EE2 at low concentrations.
author2 Zhang Zuoqi
author_facet Zhang Zuoqi
Christian, Bope Domilongo
format Theses and Dissertations
author Christian, Bope Domilongo
author_sort Christian, Bope Domilongo
title Molecular modeling and simulation for proteins and polymer membranes
title_short Molecular modeling and simulation for proteins and polymer membranes
title_full Molecular modeling and simulation for proteins and polymer membranes
title_fullStr Molecular modeling and simulation for proteins and polymer membranes
title_full_unstemmed Molecular modeling and simulation for proteins and polymer membranes
title_sort molecular modeling and simulation for proteins and polymer membranes
publishDate 2017
url http://hdl.handle.net/10356/72871
_version_ 1759853337696534528