Tube Translocation of a Herniating Chain

• Autorzy: Żurek S. , Drzewiński A.
• Konferencja: The Workshop on Current Problems in Physics: Zielona Góra – Lviv, Zielona Góra,19-21 October 2009
• Języki publikacji: EN

Abstrakty

EN

Translocation is modeled with the Rubinstein-Duke rules for hopping reptons along a one-dimensional lattice (tube). Identification of some coupled states guarantees a semi-periodicity of the process. The chain is driven through the pore by a bias potential promoting the transition of stored length in one direction. Accounting exactly for all allowed states the translocation time of polymers up to the 10-links length is determined. The crossover from reptation to faster dynamics through gradually allowing hernia creation and annihilation is found. Some computational details are presented.

Słowa kluczowe

EN

Rubinstein-Duke model; translocation; semi-periodic stochastic model

• Wydawca: Institute of Bioorganic Chemistry Scientific Publishers OWN, Polish Academy of Sciences
• Czasopismo: Computational Methods in Science and Technology
• Rocznik: 2010
• Tom: Vol. 16, No. 2
• Strony: 211--215
• Opis fizyczny: Bibliogr. 9 poz., rys.

Twórcy

autor

Żurek S.

autor

Drzewiński A.

• Institute of Physics, University of Zielona Góra, ul. Prof. Z. Szafrana 4a, 65-516 Zielona Góra, Poland,

Bibliografia

• [1] B. Albert, D. Bray, J. Lewis, M. Raff, K. Roberts, J.D. Watson, Molecular Biology of the Cell. (Garland, New York, 1994).
• [2] J.J. Kasianowicz, E. Brandin, D. Branton, D.W. Deamer, Characterization of individual polynucleotide molecules using a membrane channel. Proc. Natl. Acad. Sci. USA 93, 13770 (1996).
• [3] A. Meller, L. Nivon, D. Branton, Voltage-Driven DNA Translocations through a Nanopore. Phys. Rev. Lett. 86, 3435 (2001).
• [4] V.V. Lehtola, R.P. Linna, K. Kaski, Critical evaluation of the computational methods used in the forced polymer translocation. Phys. Rev. E78, 061803 (2008).
• [5] A. Drzewiński, J.M.J. van Leeuwen, Crossover from reptation to Rouse dynamics in a one-dimensional model, Phys. Rev. E73, 061802 (2006).
• [6] B. Widom, J.L. Viovy, A.D. Defontaines, Repton model of gel electrophoresis and diffusion. J. Phys. I France 1 (1991).
• [7] J.M.J. van Leeuwen, A. Drzewiński, Stochastic Lattice Models for the Dynamics of Linear Polymers. Phys. Rep. 475, 53 (2009).
• [8] E. Gabriel, G.E. Fagg, G. Bosilca, T. Angskun et al., Open MPI: Goals, Concept, and Design of a Next Generation MPI Implementation. Proceedings of the 11th European PVM/MPI Users’ Group Meeting, 2004.
• [9] X.S. Li, J.W. Demmel, SuperLU DIST: A Scalable Distributed-Memory Sparse Direct Solver for Unsymmetric Linear Systems. ACM Trans. Mathematical Software 29, 2 (2003).