26 research outputs found
Monte Carlo simulation of melting transition on DNA nanocompartment
DNA nanocompartment is a typical DNA-based machine whose function is
dependent of molecular collective effect. Fundamental properties of the device
have been addressed via electrochemical analysis, fluorescent microscopy, and
atomic force microscopy. Interesting and novel phenomena emerged during the
switching of the device. We have found that DNAs in this system exhibit a much
steep melting transition compared to ones in bulk solution or conventional DNA
array. To achieve an understanding to this discrepancy, we introduced DNA-DNA
interaction potential to the conventional Ising-like Zimm-Bragg theory and
Peyrard-Bishop model of DNA melting. To avoid unrealistic numerical calculation
caused by modification of the Peyrard-Bishop nonlinear Hamiltonian with the
DNA-DNA interaction, we established coarse-gained Monte Carlo recursion
relations by elucidation of five components of energy change during melting
transition. The result suggests that DNA-DNA interaction potential accounts for
the observed steep transition.Comment: 12 pages, 5 figure
Torsional fluctuations in columnar DNA assemblies
In columnar assemblies of helical bio-molecules the azimuthal degrees of
freedom, i.e. rotations about the long axes of molecules, may be important in
determining the structure of the assemblies especially when the interaction
energy between neighbouring molecules explicitly depends on their relative
azimuthal orientations. For DNA this leads to a rich variety of mesophases for
columnar assemblies, each categorized by a specific azimuthal ordering. In a
preceding paper [A. Wynveen, D. J. Lee, and A. A. Kornyshev, Eur. Phys. J. E,
16, 303 (2005)] a statistical mechanical theory was developed for the
assemblies of torsionally rigid molecues in order to determine how thermal
fluctuations influence the structure of these mesophases. Here we extend this
theory by including torsional fluctuations of the molecules, where a DNA
molecule may twist about its long axis at the cost of torsional elastic energy.
Comparing this with the previous study, we find that inclusion of torsional
fluctuations further increases the density at which the transition between the
hexagonal structure and the predicted rhombic phase occurs and reduces the
level of distortion in the rhombic phase. As X-ray diffraction may probe the
2-D lattice structure of such assemblies and provide information concerning the
underlying interaction between molecules, we have also calculated correlation
functions for the azimuthal ordering which are manifest in an x-ray scattering
intensity profiles.Comment: 33 pages, 8 figure
Phase Transitions in a Two-Component Site-Bond Percolation Model
A method to treat a N-component percolation model as effective one component
model is presented by introducing a scaled control variable . In Monte
Carlo simulations on , , and simple cubic
lattices the percolation threshold in terms of is determined for N=2.
Phase transitions are reported in two limits for the bond existence
probabilities and . In the same limits, empirical formulas
for the percolation threshold as function of one
component-concentration, , are proposed. In the limit a new
site percolation threshold, , is reported.Comment: RevTeX, 5 pages, 5 eps-figure
Rare isotope production in statistical multifragmentation
Producing rare isotopes through statistical multifragmentation is
investigated using the Mekjian method for exact solutions of the canonical
ensemble. Both the initial fragmentation and the the sequential decay are
modeled in such a way as to avoid Monte Carlo and thus provide yields for
arbitrarily scarce fragments. The importance of sequential decay, exact
particle-number conservation and the sensitivities to parameters such as
density and temperature are explored. Recent measurements of isotope ratios
from the fragmentation of different Sn isotopes are interpreted within this
picture.Comment: 10 eps figure
Phase Behavior of Columnar DNA Assemblies
The pair interaction between two stiff parallel linear DNA molecules depends
not only on the distance between their axes but on their azimuthal orientation.
The positional and orientational order in columnar B-DNA assemblies in solution
is investigated, based on the DNA-DNA electrostatic pair potential that takes
into account DNA helical symmetry and the amount and distribution of adsorbed
counterions. A phase diagram obtained by lattice sum calculations predicts a
variety of positionally and azimuthally ordered phases and bundling transitions
strongly depending on the counterion adsorption patterns.Comment: 4 pages, 3 figures, submitted to PR
Adsorption of mono- and multivalent cat- and anions on DNA molecules
Adsorption of monovalent and multivalent cat- and anions on a deoxyribose
nucleic acid (DNA) molecule from a salt solution is investigated by computer
simulation. The ions are modelled as charged hard spheres, the DNA molecule as
a point charge pattern following the double-helical phosphate strands. The
geometrical shape of the DNA molecules is modelled on different levels ranging
from a simple cylindrical shape to structured models which include the major
and minor grooves between the phosphate strands. The densities of the ions
adsorbed on the phosphate strands, in the major and in the minor grooves are
calculated. First, we find that the adsorption pattern on the DNA surface
depends strongly on its geometrical shape: counterions adsorb preferentially
along the phosphate strands for a cylindrical model shape, but in the minor
groove for a geometrically structured model. Second, we find that an addition
of monovalent salt ions results in an increase of the charge density in the
minor groove while the total charge density of ions adsorbed in the major
groove stays unchanged. The adsorbed ion densities are highly structured along
the minor groove while they are almost smeared along the major groove.
Furthermore, for a fixed amount of added salt, the major groove cationic charge
is independent on the counterion valency. For increasing salt concentration the
major groove is neutralized while the total charge adsorbed in the minor groove
is constant. DNA overcharging is detected for multivalent salt. Simulations for
a larger ion radii, which mimic the effect of the ion hydration, indicate an
increased adsorbtion of cations in the major groove.Comment: 34 pages with 14 figure
Decoration lattices of colloids adsorbed on stripepatterned substrates
The equilibrium structure of decoration lattices composed of colloidal particles adsorbed on periodic stripepatterned substrates is calculated as a function of the stripe width and separation and for different interparticle interactions. Due to a competition of length scales, a wealth of different stable decoration lattices occurs such as triangular, quadratic, rhombic, kitelike, and sheared honeycomb lattices, triangular slices as well as triangle superlattices. This is of relevance for constructing templates that enforce crystal growth of unusual solid structures