Aniket Bhattacharya

Aniket Bhattacharya


University of Central Florida

Department of Physics, Orlando, FL 32816


Monday, April 2, 2012

4:30 p.m.

Cardwell 102

How does a DNA Translocate through a Nanopore?*†


The experimental studies of voltage driven translocation of a single stranded DNA through a-hemolysin pore [1] and subsequently through silicon nano-pores 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 and separation of macromolecules in general. 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. Translocation of a polymer chain through a nanopore depends on several factors. Even for the idealized case of a narrow pore and an infinitely thin wall, it has been established how pore friction and finite chain length affect the translocation dynamics [2]. For translocation under a bias present within the pore, a fully flexible translocating chain is out-of-equilibrium and conformations at the cis and trans sides are very different [3,4]. Recently we have demonstrated these out-of-equilibrium effects by analyzing conformations of sub-chains as a function of the distance from the pore [4]. The emerging physical picture in terms of an effective Flory exponent for each subchain is consistent with the tension propagation picture first introduced by Sakaue [5]. In this talk I will first discuss various non-equilibrium aspects for a fully flexible translocating chain. I will then discuss how semi-flexibility affects these results [6]. Finally, I will discuss how dwell time of the individual monomers (nucleotides)can provide novel key for detecting sequences [7].


*Partially supported by a NSF-CHEM grant.

†Work done in collaboration with Prof. Kurt Binder, Prof. Wokyung Sung, Prof. Andrey Milchev, Prof. Tapio Ala-Nissila and Timo Ikonen.

[1] J.J. Kasianowicz, E. Brandin, D. Branton, and D.W. Deamer, Proc. Natl. Acad. Sci. U.S.A. 93, 13770 (1996).

[2] T. Ikonen, A. Bhattacharya, T. Ala-Nissila and W. Sung, “Unifying model of driven polymer translocation”(submitted to Phys. Rev. E).

[3] Aniket Bhattacharya, Heath Morrison, Kaifu Luo, Tapio Ala-Nissila, See-Chen Ying, Andrey Milchev and Kurt Binder, “Scaling of Driven Polymer Translocation through a nanopore”, Eur. Phys. J. E 29, 423 (2009).

[4] Aniket Bhattacharya and Kurt Binder, “Out-of-equilibrium aspects of a translocating chain through a nanopore”, Phys. Rev. E 81, 041804(2010).

[5] T. Sakaue, Phys. Rev. E 76, 021803 (2007); ibid. 81,041808 (2010).

[6] Aniket Bhattacharya, “Translocation dynamics of a semi-flexible Chain” (under preparation).

[7] Kaifu Luo, Tapio Ala-Nissila, S-C Ying, and Aniket Bhattacharya, Phys. Rev. Lett. 99, 148102 (2007); ibid. 100, 1058101 (2008).