Quantized current blockade and hydrodynamic correlations in biopolymer translocation through nanopores: evidence from multiscale simulations

arXiv:0802.1107v1 [physics.comp-ph] 8 Feb 2008 Quantized current blockade and hydrodynamic correlations in biopolymer translocation through nanopores: evidence from multiscale simulations Massimo Bernaschi1, Simone Melchionna2, Sauro Succi1, Maria Fyta3, and Efthimios Kaxiras3 1 Istituto Applicazioni Calcolo, CNR, Viale del Policlinico 137, 00161, Roma, Italy 2 INFM-SOFT, Department of Physics, Universit`a di Roma La Sapienza, P.le A. Moro 2, 00185 Rome, Italy 3 Department of Physics and School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA (Dated: October 31, 2018) We present a detailed description of biopolymer translocation through a nanopore in the presence of a solvent, using an innovative multi-scale methodology which treats the biopolymer at the micro- scopic scale as combined with a self-consistent mesoscopic description for the solvent fluid dynamics. We report evidence for quantized current blockade depending on the folding configuration and of- fer detailed information on the role of hydrodynamic correlations in speeding-up the translocation process. Biopolymer translocation through nanoscale pores holds the promise of efficient and improved sensing for many applications in biotechnology, and possibly ultra- fast DNA sequencing [1, 2, 3]. Recent advances in fab- rication of solid-state nanopores [4, 5] have spurred de- tailed experimental studies of the translocation process, with DNA as the prototypical biopolymer of interest [6]. Computer simulations that can account for the complex- ity of the biomolecule motion as it undergoes translo- cation, as well as its interaction with the environment (the nanopore and the solvent), are crucial in elucidat- ing current experiments [7, 8] and possibly inspiring new ones. Here, we study the dynamical, statistical and syn- ergistic features of the translocation process of a biopoly- mer through a nanopore by a multiscale method based on molecular dynamics for the biopolymer motion and mesoscopic lattice Boltzmann dynamics for the solvent. We report evidence for quantized current blockade de- pending on the folding configuration (single- or multi-file translocation) in good agreement with recent experimen- tal observations [7]. Our simulations show the signifi- cance of hydrodynamic correlations in speeding-up the translocation process. Nanopores are an essential element of cells and mem- branes, controlling the passage of molecules and regulat- ing many biological processes such as viral infection by phages and inter-bacterial DNA transduction [9]. The last two decades have witnessed the emergence of artifi- cial solid-state nanopores as potential devices for sensing biomolecules through novel means [6]. One of the most intriguing possibilities is ultra-fast sequencing of DNA by measuring the electronic signal as the biomolecule translocates through a nanopore decorated with elec- trodes [3]. While this goal still remains elusive, a num- ber of detailed studies on DNA translocation through nanopores have been reported recently [7, 8]. These ex- periments typically measure the blockade of the ion cur- rent through the nanopore during the time it takes the molecule to translocate, which provides statistical infor- mation about the biomolecule motion during the process. Numerical simulation of the translocation process pro- vides a wealth of information complementary to experi- ments, but is hindered by the very large number of par- ticles involved in the full process: these include all the atoms that constitute the biomolecule, the molecules and ions that constitute the solvent, and the atoms that are part of the solid membrane in the nanopore region. The spatial and temporal extent of the full system on atomic scales is far beyond what can be handled by direct com- putational methods without introducing major approxi- mations. Some universal features of translocation have been analyzed by means of suitably simplified statisti- cal schemes [10], and non-hydrodynamic coarse-grained or microscopic models [11, 12, 13] or other mesoscopic approaches [14]. Many atomic degrees of freedom, and especially those of the solvent and the membrane wall, are uninteresting from the biological point of view. The problem naturally calls for a multi-scale computational approach that can elucidate the interesting experimental measurements while coarse-graining the less important degrees of freedom. We have developed a multiscale method for treating the dynamics of biopolymer translocation [15] and per- formed an extensive set of numerical simulations, com- bining constrained molecular dynamics (MD) for the polymer motion with a Lattice-Boltzmann (LB) treat- ment of the solvent hydrodynamics [16]. The biopoly- mer transits through a nanopore under the effect of a localized electric field applied across the pore, mimicking the experimental setup [8]. The simulations provide di- rect computational evidence of quantized current block- ade and confirm the experim

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