78 research outputs found
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 ) and bow- or banana-shaped molecules (hard spherocylinder dimers
with length/breadth ratio or 2.5 and opening angle ) to
probe the molecular-scale organization and phase behavior of rod/banana
mixtures. We find that a low concentration (3%) of dimers
induces anticlinic (SmC) ordering in an untilted smectic (SmA) phase for
. For smaller , half of each bow-shaped
molecule is nanophase segregated between smectic layers, and the smectic layers
are untilted. For , no tilted phases are induced. However,
with decreasing 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 . 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 . With decreasing , a transition
from a nonpolar to a polar smectic phase is observed near ,
and the nematic phase becomes thermodynamically unstable for . 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
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