2009 APS March Meeting
Volume 54, Number 1
Monday–Friday, March 16–20, 2009;
Pittsburgh, Pennsylvania
Session B4: Polymer Translocation
11:15 AM–1:51 PM,
Monday, March 16, 2009
Room: 306/307
Sponsoring
Unit:
DPOLY
Chair: Murugappan Muthukumar, University of Massachusetts
Abstract ID: BAPS.2009.MAR.B4.3
Abstract: B4.00003 : Simulation studies of DNA translocation through a nanopore ($^\dagger$)
12:27 PM–1:03 PM
Preview Abstract
Abstract
Author:
Aniket Bhattacharya
(University of Central Florida)
The experimental studies of voltage driven translocation
of a single stranded DNA through a $\alpha$-hemolysin pore,
have stimulated a lot of activities as the phenomenon is rich
in fundamental science involved and its prospective technical
applications for detecting
DNA/RNA sequences. While it is the attributes of heteropolymer
translocation that are
the key ingredients for prospective
new sequencing methods, these experiments have generated
stimulating theoretical and
numerical studies directed toward a seemingly much simpler
problem of homopolymer translocation
through a nanopore. The earlier theoretical work of Muthukumar,
Sung and Park, and
by Kardar and his collaboartors$^2$ have been supplemented by
more recent theoretical
work by Dubbledam \textit{et. al} and Panja \textit{et. al}$^3$.
During this talk I will show results from Langevin dynamics
simulation carried out on a
coarse-garined bead-spring model of DNA-polymer both for the
unbiased and driven
translocation$^4$.
During the first part of the talk, after a brief review of the
current
theories of DNA translocation, specifically mentioning the
underlying assumptions,
I will compare simulation results with those predicted by
different theories.
Particularly, I will show
numerical results for the translocation exponent $\alpha$ defined as
$\langle \tau \rangle \sim N^\alpha$ and the exponent for the
$s$-coordinate
$\beta$ defined as $\langle s^2(\tau) \rangle \sim \tau^\beta$,
and discuss how the numerical
values differ as one chooses slightly different pore width and
geometry.
In the second part of my talk I show how a model
\textit{attractive nanopore} can
distinguish the sequence of a heteropolymer$^4$ and discuss
possibility of making a
device based on this idea. \\
$^\dagger${work done in collaboration with Kaifu Luo, Tapio
Ala-Nissila, See-chen Yin, Andrey
Milchev and Kurt Binder}\\
$^1$J. J. Kasianowiczs, E. Brandin, D. Branton and D. W. Deamer,
\textit{Proc. Natl. Acad. Sci. U.S.A.} {\bf 93}, 13770 (1996).\\
$^2$W. Sung and P. J. Park, \textit{Phys. Rev. Lett.} {\bf 77},
783 (1996);
M. Muthukumar, \textit{J. Chem. Phys.} {\bf 111}, 10371 (1999);
J. Chuang, Y. Kantor and M. Kardar, \textit{Phys. Rev. E} {\bf
65}, 011802 (2001);
Y. Kantor and M. Kardar, \textit{Phys. Rev. E} {\bf 69}, 021806
(2004).\\
$^3$J. L. A. Dubbeldam, A. Milchev, V. G. Rostiashvili, and T.
A. Vilgis,
\textit{Phys. Rev. E} {\bf 76}, 010801(R) (2007);
\textit{Europhys. Lett.} {\bf 79}, 18002 (2007); D. Panja, G. T.
Barkema,
and R. C. Ball, \textit{J. Phys.: Condens. Matter} {\bf 20},
075101 (2008); H. Vocks, D. Panja, G. T. Barkema, and R. C. Ball,
\textit{J. Phys.: Condens. Matter} {\bf 20}, 095224 (2008).
\\
$^4$ K. F. Luo, I. Huopaniemi, T. Ala-Nissila, P. Pomorski, M.
Karttunen, S. C. Ying,
and A. Bhattacharya, \textit{Phys. Rev. E} {\bf }, 050901(R) (2008);
A. Bhattacharya, H. Morrison, K. F. Luo, T. Ala-Nissila, S. C.
Ying, A. Milchev, and K. Binder,
arXiv:0808.1868v3 (2008). \\
$^5$ K. F. Luo, T. Ala-Nissila, S. C. Ying, and A. Bhattacharya,
\textit{J. Chem. Phys.} {\bf 126}, 145101 (2007),
\textit{Phys. Rev. Lett.} {\bf 99}, 148102 (2007),
\textit{Phys. Rev. Lett.} {\bf 99}, 058101 (2008).
To cite this abstract, use the following reference: http://meetings.aps.org/link/BAPS.2009.MAR.B4.3