“Coarse Grained" Bead Modeling of Macromolecules Transport in Free Solution and in a Gel

The modeling of transport behavior of charged particles carried out in our laboratory is based on classical continuum electro kinetic theory. It is applied to a variety of systems from small electrolyte ions to macromolecules including peptides, DNA and nanoparticles. Systems range from weakly charg...

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Main Author: Wu, Hengfu
Format: Others
Published: ScholarWorks @ Georgia State University 2014
Subjects:
Gel
Online Access:http://scholarworks.gsu.edu/chemistry_diss/98
http://scholarworks.gsu.edu/cgi/viewcontent.cgi?article=1103&context=chemistry_diss
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spelling ndltd-GEORGIA-oai-scholarworks.gsu.edu-chemistry_diss-11032016-01-22T03:41:06Z “Coarse Grained" Bead Modeling of Macromolecules Transport in Free Solution and in a Gel Wu, Hengfu The modeling of transport behavior of charged particles carried out in our laboratory is based on classical continuum electro kinetic theory. It is applied to a variety of systems from small electrolyte ions to macromolecules including peptides, DNA and nanoparticles. Systems range from weakly charged particles to highly charged ones. Transport properties studied include conductance, electrophoresis, and diffusion. In this dissertation, the conductance of polyvalent electrolytes ions is studied both by a “small ion” model [R.M. Fuoss, L. Onsager, J. Phys. Chem. 61 (1957) 668] and “large ion” model [R.W. O’Brien, L.R. White, J. Chem. Soc. Faraday Trans. 2 (74) (1978) 1607)]. Also, the coarse-grained continuum primitive model is developed and used to characterize the titration and electrical conductance behavior of aqueous solutions of fullerene hexa-malonic acid, which is a highly charged electrolyte with an absolute valence charge as high as 12. Free solution electrophoresis is closely related to conductance and a coarse-grained bead modeling methodology, BMM, developed in the Allison’s laboratory starting in 2006, is generalized to characterize peptide systems with respect to the charge, conformation, and possibly specific interactions with components of the BGE. For weakly charged peptides, the electrostatic potential is treated at the level of linear Poisson-Boltzmann equation, which predicts the electrophoretic mobility with considerable accuracy [S. Allison, H. Pei, U. Twahir, H. Wu, J. Sep. Sci., 2010, 33(16):2430-2438], but fails for highly charged systems. A new nonlinear Poisson-Boltzmann, NLPB-BM procedure is developed and applied to the free solution electrophoretic mobility of low molecular mass oligolysines. The difficulty of highly charged systems is twofold: more complex handeling of electrostatics and accounting for the relaxation effect. Both issues are addressed in this dissertation. A related problem we investigated deals with the retarding influence of a gel on the rotational motion of a macromolecule. This is investigated within the framework of the Effective Medium (EM) model and is applied to examine the electric birefringence decay of a 622 base pair DNA fragment in an agarose gel. Modeling is also compared with experiment. 2014-08-12T07:00:00Z text application/pdf http://scholarworks.gsu.edu/chemistry_diss/98 http://scholarworks.gsu.edu/cgi/viewcontent.cgi?article=1103&context=chemistry_diss Chemistry Dissertations ScholarWorks @ Georgia State University Electrophoresis Conductance Diffusion Coarse-Grained Effective Medium Relaxation Correction Complex formation Gel
collection NDLTD
format Others
sources NDLTD
topic Electrophoresis
Conductance
Diffusion
Coarse-Grained
Effective Medium
Relaxation Correction
Complex formation
Gel
spellingShingle Electrophoresis
Conductance
Diffusion
Coarse-Grained
Effective Medium
Relaxation Correction
Complex formation
Gel
Wu, Hengfu
“Coarse Grained" Bead Modeling of Macromolecules Transport in Free Solution and in a Gel
description The modeling of transport behavior of charged particles carried out in our laboratory is based on classical continuum electro kinetic theory. It is applied to a variety of systems from small electrolyte ions to macromolecules including peptides, DNA and nanoparticles. Systems range from weakly charged particles to highly charged ones. Transport properties studied include conductance, electrophoresis, and diffusion. In this dissertation, the conductance of polyvalent electrolytes ions is studied both by a “small ion” model [R.M. Fuoss, L. Onsager, J. Phys. Chem. 61 (1957) 668] and “large ion” model [R.W. O’Brien, L.R. White, J. Chem. Soc. Faraday Trans. 2 (74) (1978) 1607)]. Also, the coarse-grained continuum primitive model is developed and used to characterize the titration and electrical conductance behavior of aqueous solutions of fullerene hexa-malonic acid, which is a highly charged electrolyte with an absolute valence charge as high as 12. Free solution electrophoresis is closely related to conductance and a coarse-grained bead modeling methodology, BMM, developed in the Allison’s laboratory starting in 2006, is generalized to characterize peptide systems with respect to the charge, conformation, and possibly specific interactions with components of the BGE. For weakly charged peptides, the electrostatic potential is treated at the level of linear Poisson-Boltzmann equation, which predicts the electrophoretic mobility with considerable accuracy [S. Allison, H. Pei, U. Twahir, H. Wu, J. Sep. Sci., 2010, 33(16):2430-2438], but fails for highly charged systems. A new nonlinear Poisson-Boltzmann, NLPB-BM procedure is developed and applied to the free solution electrophoretic mobility of low molecular mass oligolysines. The difficulty of highly charged systems is twofold: more complex handeling of electrostatics and accounting for the relaxation effect. Both issues are addressed in this dissertation. A related problem we investigated deals with the retarding influence of a gel on the rotational motion of a macromolecule. This is investigated within the framework of the Effective Medium (EM) model and is applied to examine the electric birefringence decay of a 622 base pair DNA fragment in an agarose gel. Modeling is also compared with experiment.
author Wu, Hengfu
author_facet Wu, Hengfu
author_sort Wu, Hengfu
title “Coarse Grained" Bead Modeling of Macromolecules Transport in Free Solution and in a Gel
title_short “Coarse Grained" Bead Modeling of Macromolecules Transport in Free Solution and in a Gel
title_full “Coarse Grained" Bead Modeling of Macromolecules Transport in Free Solution and in a Gel
title_fullStr “Coarse Grained" Bead Modeling of Macromolecules Transport in Free Solution and in a Gel
title_full_unstemmed “Coarse Grained" Bead Modeling of Macromolecules Transport in Free Solution and in a Gel
title_sort “coarse grained" bead modeling of macromolecules transport in free solution and in a gel
publisher ScholarWorks @ Georgia State University
publishDate 2014
url http://scholarworks.gsu.edu/chemistry_diss/98
http://scholarworks.gsu.edu/cgi/viewcontent.cgi?article=1103&context=chemistry_diss
work_keys_str_mv AT wuhengfu coarsegrainedbeadmodelingofmacromoleculestransportinfreesolutionandinagel
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