Bulletin of the American Physical Society
2009 APS March Meeting
Volume 54, Number 1
Monday–Friday, March 16–20, 2009; Pittsburgh, Pennsylvania
Session B4: Polymer Translocation |
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Sponsoring Units: DPOLY Chair: Murugappan Muthukumar, University of Massachusetts Room: 306/307 |
Monday, March 16, 2009 11:15AM - 11:51AM |
B4.00001: Polymer Translocation: What Can We Learn From An Exactly Solvable One-Dimensional Model? Invited Speaker: The translocation of a polymer through a narrow hole or channel is generally not a quasi-static process (as we have shown using a detailed Molecular Dynamics simulation with explicit solvent). Nevertheless, numerous analytical models have relied on this approximation/assumption in order to make progress. A simple approach is then to describe the problem in terms of the translocation coordinate (e.g., the number of monomer on the \textit{trans} side of the wall), which effectively makes it a one-dimensional problem with an external driving field and a entropy-related potential landscape. Our group has exploited this simple idea to its fullest using a lattice Monte-Carlo-like model that provides exact numerical results, even for extremely rare events. In this presentation, I will explain how this simplified model is built and how it can be modified to include a variety of additional effects such as polymer stiffness or the differences between the various monomer types in a biopolymer like DNA. I will review the main results obtained to date, focusing on the transitions between the low- and high- field regimes, and between the short- and long- polymer chain limits. Finally, I will examine the role of attractive interactions between the polymer and specific sites inside the channel. [Preview Abstract] |
Monday, March 16, 2009 11:51AM - 12:27PM |
B4.00002: DNA translocation through small channels and pores from molecular models. Hydrodynamic, electrostatic, and hybridization considerations. Invited Speaker: The flow and translocation of long DNA molecules are of considerable applied and fundamental interest. Design of effective genomic devices requires control of molecular shape and positioning at the level of microns and nanometers, and understanding the manner in which DNA is packaged into small channels and cavities is of interest to biology and medicine. This presentation will present an overview of hierarchical models and computational approaches developed by our research group to investigate the effects of confinement, hydrodynamic interactions, and salt concentration, on the structure and properties of DNA, both at equilibrium and beyond equilibrium. The talk will include a discussion of coarse grain descriptions of the flow of DNA in microfluidic and nanofluidic channels over multiple length and time scales, and a discussion of emerging, detailed models that are capable of describing melting and rehybridization at the single nucleotide level, as well as the packaging of DNA into viral capsids and small pores. [Preview Abstract] |
Monday, March 16, 2009 12:27PM - 1:03PM |
B4.00003: Simulation studies of DNA translocation through a nanopore ($^\dagger$) Invited Speaker: 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). [Preview Abstract] |
Monday, March 16, 2009 1:03PM - 1:39PM |
B4.00004: Anomalous dynamics of polymer translocation Invited Speaker: We study the passage times of a translocating polymer of length $N$ in three dimensions, while it passes through a narrow pore. We show that the behavior of the polymer stems from the polymer dynamics at the immediate vicinity of the pore --- in particular, the memory effects in the polymer chain tension imbalance across the pore. We take as a reaction coordinate the number $s$ of the monomer residing in the pore. in the case of unbiased translocation, these memory effects cause the mobility of $s$ to be anomalous diffusion for times up to the Rouse time $N\sim N^{1+2\nu}$ or Zimm time $N\sim N^{3\nu}$, without or with hydrodynamics, respectively. Here, $\nu$ is the Flory exponent. Beyond this time, the dynamics becomes ordinary diffusion. As a consequence, the pore blockade time scales with length as $\tau_d \sim N^{2+\nu}$. If a force of sufficient strength is pulling on one end, the pore blockade time scales as $\tau_d \sim N^2$ in the absence of hydrodynamics. If a voltage is applied across the pore, which drives the charged polymer, the pore blockade time scales as $\tau_d \sim N^{(1+2\nu)/(1+\nu)}$ without, and $\tau_d \sim N^{3\nu/(1+\nu)}$ with hydrodynamics. In these cases, the pore blockade time decreases inversely with force and field strength, respectively. Our theoretical framework is substantiated with high-precision computer simulations. We will show that memory effects similar to those governing translocation, also play a role in the dynamics of dense polymer solutions and polymer melts. [Preview Abstract] |
Monday, March 16, 2009 1:39PM - 1:51PM |
B4.00005: Polyelectrolyte Translocation Murugappan Muthukumar Theoretical considerations of relative contributions from electrostatic and entropic barriers will be addressed for the phenomenon of polymer translocation through alpha-hemolysin pores. [Preview Abstract] |
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