Coarse-grained simulation of polymer translocation through an artificial nanopore

The translocation of a macromolecule through a nanometer-sized pore is an interesting process with important applications in the development of biosensors for single--molecule analysis and in drug delivery and gene therapy. We have carried out a molecular dynamics simulation study of electrophoretic translocation of a charged polymer through an artificial nanopore to explore the feasibility of semiconductor--based nanopore devices for ultra--fast DNA sequencing. The polymer is represented by a simple bead--spring model designed to yield an appropriate coarse-grained description of the phosphate backbone of DNA in salt--free aqueous solution. A detailed analysis of single translocation event is presented to assess whether the passage of individual ions through the pore can be detected by a nanoscale field--effect transistor by measuring variations in electrostatic potential during polymer translocation. We find that it is possible to identify single events corresponding to the passage of counterions through the pore, but that discrimination of individual ions on the polymer chain based on variations in electrostatic potential is problematic. Several distinct stages in the translocation process are identified, characterized by changes in polymer conformation and by variations in the magnitude and direction of the internal electric field induced by the fluctuating charge distribution. The dependence of the condensed fraction of counterions on Bjerrum length leads to significant changes in polymer conformation, which profoundly affect the dynamics of electrophoresis and translocation.Comment: 37 pages Revtex, 11 postscript figure

Collapse of Double-Walled Carbon Nanotube Bundles under Hydrostatic Pressure

We use classical molecular dynamics simulations to study the collapse of single (SWNT) and double-walled (DWNT) carbon nanotube bundles under hydrostatic pressure. The collapse pressure (pc) varies as 1/R^3, where R is the SWNT radius or the DWNT effective radius. The bundles show ~ 30% hysteresis and the hexagonally close packed lattice is completely restored on decompression. The pc of DWNT is found to be close to the sum of its values for the inner and the outer tubes considered separately as SWNT, demonstrating that the inner tube supports the outer tube and that the effective bending stiffness of DWNT, D(DWNT) ~ 2D(SWNT) . We use an elastica formulation to derive the scaling and the collapse behavior of DWNT and multi-walled carbon nanotubes.Comment: This paper has been accepted for publication in Physical Review B. After publication, it will be available at http://prb.aps.org

Induced Anticlinic Ordering and Nanophase Segregation of Bow-Shaped Molecules in a Smectic Solvent

Recent experiments indicate that doping low concentrations of bent-core molecules into calamitic smectic solvents can induce anticlinic and biaxial smectic phases. We have carried out Monte Carlo (MC) simulations of mixtures of rodlike molecules (hard spherocylinders with length/breadth ratio $L_{\rm rod}/D = 5$) and bow- or banana-shaped molecules (hard spherocylinder dimers with length/breadth ratio $L_{ban}/D = 5$ or 2.5 and opening angle $\psi$) to probe the molecular-scale organization and phase behavior of rod/banana mixtures. We find that a low concentration (3%) of $L_{ban}/D = 5$ dimers induces anticlinic (SmC$_A$) ordering in an untilted smectic (SmA) phase for $100^\circ \le \psi < 150^\circ$. For smaller $\psi$, half of each bow-shaped molecule is nanophase segregated between smectic layers, and the smectic layers are untilted. For $L_{ban}/D = 2.5$, no tilted phases are induced. However, with decreasing $\psi$ we observe a sharp transition from {\sl intralamellar} nanophase segregation (bow-shaped molecules segregated within smectic layers) to {\sl interlamellar} nanophase segregation (bow-shaped molecules concentrated between smectic layers) near $\psi = 130^\circ$. These results demonstrate that purely entropic effects can lead to surprisingly complex behavior in rod/banana mixtures.Comment: 5 pages Revtex, 7 postscript figure

Phase Behavior of Bent-Core Molecules

Recently, a new class of smectic liquid crystal phases (SmCP phases) characterized by the spontaneous formation of macroscopic chiral domains from achiral bent-core molecules has been discovered. We have carried out Monte Carlo simulations of a minimal hard spherocylinder dimer model to investigate the role of excluded volume interations in determining the phase behavior of bent-core materials and to probe the molecular origins of polar and chiral symmetry breaking. We present the phase diagram as a function of pressure or density and dimer opening angle $\psi$. With decreasing $\psi$, a transition from a nonpolar to a polar smectic phase is observed near $\psi = 167^{\circ}$, and the nematic phase becomes thermodynamically unstable for $\psi < 135^{\circ}$. No chiral smectic or biaxial nematic phases were found.Comment: 4 pages Revtex, 3 eps figures (included

Morphology control of PEDOT:PSS polyelectrolyte by hard-cation-soft-anion ionic liquids: Microscopic observation by molecular dynamics simulation

International audienc

PEDOT:PSS morphology controlled by hard-cation-soft-anion ionic liquids: Multiscale molecular modeling of disordered molecular assemblies at atomic details

International audienc

Interactions between the Molecular Components of the Cowpea Chlorotic Mottle Virus Investigated by Molecular Dynamics Simulations

International audienc