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Brownian dynamics simulation of dilu...

Jain, Semant.

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Brownian dynamics simulation of dilute polymer chains.

Record Type:	Language materials, printed : Monograph/item
Title/Author:	Brownian dynamics simulation of dilute polymer chains./
Author:	Jain, Semant.
Description:	102 p.
Notes:	Adviser: Ronald G. Larson.
Contained By:	Dissertation Abstracts International69-03B.
Subject:	Chemistry, Polymer. -
Online resource:	http://pqdd.sinica.edu.tw/twdaoapp/servlet/advanced?query=3304993
ISBN:	9780549509493

Brownian dynamics simulation of dilute polymer chains.
Jain, Semant.

Brownian dynamics simulation of dilute polymer chains. - 102 p.

Adviser: Ronald G. Larson.

Thesis (Ph.D.)--University of Michigan, 2008.

Local motion of polymers is extremely important while studying the behavior of single strand DNA in DNA unzipping and replication, understanding rheological properties of polymers in confined in narrow gaps for head-disk interface design for hard disk drives, and designing membrane structure for small molecule permeation through a dense polymeric membrane. So, in order to understand the mechanism of energy dissipation of dilute polymer solutions at high frequencies, I carry out a Brownian dynamics study of a linear bead-spring chain in which the beads represent individual backbone atoms, a stiff Fraenkel spring potential maintains the distance between atoms near 1.53 A, a bending potential maintains tetrahedral bonding angles, a torsional potential imposes realistic barriers to torsional transitions, and white noise represents the Brownian force from the solvent. With this model, I find that the end-to-end vector autocorrelation function from the simulation is in excellent agreement with the theoretical Rouse model predictions. Nevertheless, the autocorrelation function of the bond orientation vectors---which delineates the relaxation of the stress tensor---exhibits a much slower decay then predicted by the coarse-grain Rouse theory except near the longest relaxation time even for chains with as many as 50 bonds. I find that both the bending and torsional potentials slow down the contributions of local relaxation modes, bringing the relaxation of short chains (less than 50 bonds) closer to single exponential behavior than to the Rouse spectrum, in qualitative agreement with observations of birefringence relaxation [Lodge et al. (1982) J. Poly. Sci. 20, 1409]. Also, my normal mode predictions using the bead-spring model provides an excellent fit to data for 2400 and 6700 base single-strand DNA molecules [Shusterman et al. (2004) Phy. Rev. Lett. 92(4), 048303] and the fit yields 12 Kuhn steps per spring and a value of 0.12 for the standard hydrodynamic interaction parameter---very close to the values typical of conventional polymers such as polystyrene. Thus, my results are generally in agreement with a recent notion of a "dynamical Kuhn length" in which torsional barriers to chain motion, can suppress high frequency contribution to viscoelasticity [Larson (2004) Macromol. 37, 5110].

ISBN: 9780549509493Subjects--Topical Terms:

1018428
Chemistry, Polymer.

Brownian dynamics simulation of dilute polymer chains.
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008 110617s2008 ||||||||||||||||| ||eng d
020 $a 9780549509493
035 $a (UMI)AAI3304993
035 $a AAI3304993
040 $a UMI $c UMI
100 1 $a Jain, Semant. $3 1275826
245 1 0 $a Brownian dynamics simulation of dilute polymer chains.
300 $a 102 p.
500 $a Adviser: Ronald G. Larson.
500 $a Source: Dissertation Abstracts International, Volume: 69-03, Section: B, page: 1782.
502 $a Thesis (Ph.D.)--University of Michigan, 2008.
520 $a Local motion of polymers is extremely important while studying the behavior of single strand DNA in DNA unzipping and replication, understanding rheological properties of polymers in confined in narrow gaps for head-disk interface design for hard disk drives, and designing membrane structure for small molecule permeation through a dense polymeric membrane. So, in order to understand the mechanism of energy dissipation of dilute polymer solutions at high frequencies, I carry out a Brownian dynamics study of a linear bead-spring chain in which the beads represent individual backbone atoms, a stiff Fraenkel spring potential maintains the distance between atoms near 1.53 A, a bending potential maintains tetrahedral bonding angles, a torsional potential imposes realistic barriers to torsional transitions, and white noise represents the Brownian force from the solvent. With this model, I find that the end-to-end vector autocorrelation function from the simulation is in excellent agreement with the theoretical Rouse model predictions. Nevertheless, the autocorrelation function of the bond orientation vectors---which delineates the relaxation of the stress tensor---exhibits a much slower decay then predicted by the coarse-grain Rouse theory except near the longest relaxation time even for chains with as many as 50 bonds. I find that both the bending and torsional potentials slow down the contributions of local relaxation modes, bringing the relaxation of short chains (less than 50 bonds) closer to single exponential behavior than to the Rouse spectrum, in qualitative agreement with observations of birefringence relaxation [Lodge et al. (1982) J. Poly. Sci. 20, 1409]. Also, my normal mode predictions using the bead-spring model provides an excellent fit to data for 2400 and 6700 base single-strand DNA molecules [Shusterman et al. (2004) Phy. Rev. Lett. 92(4), 048303] and the fit yields 12 Kuhn steps per spring and a value of 0.12 for the standard hydrodynamic interaction parameter---very close to the values typical of conventional polymers such as polystyrene. Thus, my results are generally in agreement with a recent notion of a "dynamical Kuhn length" in which torsional barriers to chain motion, can suppress high frequency contribution to viscoelasticity [Larson (2004) Macromol. 37, 5110].
590 $a School code: 0127.
650 4 $a Chemistry, Polymer. $3 1018428
650 4 $a Engineering, Chemical. $3 1018531
690 $a 0495
690 $a 0542
710 2 $a University of Michigan. $3 777416
773 0 $t Dissertation Abstracts International $g 69-03B.
790 $a 0127
790 1 0 $a Larson, Ronald G., $e advisor
791 $a Ph.D.
792 $a 2008
856 4 0 $u http://pqdd.sinica.edu.tw/twdaoapp/servlet/advanced?query=3304993