1,183 research outputs found
Short DNA persistence length in a mesoscopic helical model
The flexibility of short DNA chains is investigated via computation of the
average correlation function between dimers which defines the persistence
length. Path integration techniques have been applied to confine the phase
space available to base pair fluctuations and derive the partition function.
The apparent persistence lengths of a set of short chains have been computed as
a function of the twist conformation both in the over-twisted and the untwisted
regimes, whereby the equilibrium twist is selected by free energy minimization.
The obtained values are significantly lower than those generally attributed to
kilo-base long DNA. This points to an intrinsic helix flexibility at short
length scales, arising from large fluctuational effects and local bending, in
line with recent experimental indications. The interplay between helical
untwisting and persistence length has been discussed for a heterogeneous
fragment by weighing the effects of the sequence specificities through the
non-linear stacking potential
Polaron Mass and Electron-Phonon Correlations in the Holstein Model
The Holstein Molecular Crystal Model is investigated by a strong coupling
perturbative method which, unlike the standard Lang-Firsov approach, accounts
for retardation effects due to the spreading of the polaron size. The effective
mass is calculated to the second perturbative order in any lattice
dimensionality for a broad range of (anti)adiabatic regimes and electron-phonon
couplings. The crossover from a large to a small polaron state is found in all
dimensionalities for adiabatic and intermediate adiabatic regimes. The phonon
dispersion largely smooths such crossover which is signalled by polaron mass
enhancement and on site localization of the correlation function. The notion of
self-trapping together with the conditions for the existence of light polarons,
mainly in two- and three-dimensions, are discussed. By the imaginary time path
integral formalism I show how non local electron-phonon correlations, due to
dispersive phonons, renormalize downwards the {\it e-ph} coupling justifying
the possibility for light and essentially small 2D Holstein polarons.Comment: Advances in Condensed Matter Physics (2009). Special Issue on
"Phonons and Electron Correlations in High-Temperature and Other Novel
Superconductors
J-factors of short DNA molecules
The propensity of short DNA sequences to convert to the circular form is
studied by a mesoscopic Hamiltonian method which incorporates both the bending
of the molecule axis and the intrinsic twist of the DNA strands. The base pair
fluctuations with respect to the helix diameter are treated as path
trajectories in the imaginary time path integral formalism. The partition
function for the sub-ensemble of closed molecules is computed by imposing chain
ends boundary conditions both on the radial fluctuations and on the angular
degrees of freedom. The cyclization probability, the J-factor, proves to be
highly sensitive to the stacking potential, mostly to its nonlinear parameters.
We find that the J-factor generally decreases by reducing the sequence length (
N ) and, more significantly, below N = 100 base pairs. However, even for very
small molecules, the J-factors remain sizeable in line with recent experimental
indications. Large bending angles between adjacent base pairs and anharmonic
stacking appear as the causes of the helix flexibility at short length scales.Comment: The Journal of Chemical Physics - May 2016 ; 9 page
Twist versus Nonlinear Stacking in Short DNA Molecules
The denaturation of the double helix is a template for fundamental biological
functions such as replication and transcription involving the formation of
local fluctuational openings. The denaturation transition is studied for
heterogeneous short sequences of DNA, i.e. base pairs, in the
framework of a mesoscopic Hamiltonian model which accounts for the helicoidal
geometry of the molecule. The theoretical background for the application of the
path integral formalism to predictive analysis of the molecule thermodynamical
properties is discussed. The base pair displacements with respect to the ground
state are treated as paths whose temperature dependent amplitudes are governed
by the thermal wavelength. The ensemble of base pairs paths is selected, at any
temperature, consistently with both the model potential and the second law of
thermodynamics. The partition function incorporates the effects of the base
pair thermal fluctuations which become stronger close to the denaturation. The
transition appears as a gradual phenomenon starting from the molecule segments
rich in adenine-thymine base pairs. Computing the equilibrium thermodynamics,
we focus on the interplay between twisting of the complementary strands around
the molecule axis and nonlinear stacking potential: it is shown that the latter
affects the melting profiles only if the rotational degrees of freedom are
included in the Hamiltonian. The use of ladder Hamiltonian models for the DNA
complementary strands in the pre-melting regime is questioned.Comment: Journal of Theoretical Biology (2014
Helix untwisting and bubble formation in circular DNA
The base pair fluctuations and helix untwisting are examined for a circular
molecule. A realistic mesoscopic model including twisting degrees of freedom
and bending of the molecular axis is proposed. The computational method, based
on path integral techniques, simulates a distribution of topoisomers with
various twist numbers and finds the energetically most favorable molecular
conformation as a function of temperature. The method can predict helical
repeat, openings loci and bubble sizes for specific sequences in a broad
temperature range. Some results are presented for a short DNA circle recently
identified in mammalian cells.Comment: The Journal of Chemical Physics, vol. 138 (2013), in pres
Thermodynamics of Twisted DNA with Solvent Interaction
The imaginary time path integral formalism is applied to a nonlinear
Hamiltonian for a short fragment of heterogeneous DNA with a stabilizing
solvent interaction term. Torsional effects are modeled by a twist angle
between neighboring base pairs stacked along the molecule backbone. The base
pair displacements are described by an ensemble of temperature dependent paths
thus incorporating those fluctuational effects which shape the multisteps
thermal denaturation. By summing over base pair paths, a
large number of double helix configurations is taken into account consistently
with the physical requirements of the model potential. The partition function
is computed as a function of the twist. It is found that the equilibrium twist
angle, peculiar of B-DNA at room temperature, yields the stablest helicoidal
geometry against thermal disruption of the base pair hydrogen bonds. This
result is corroborated by the computation of thermodynamical properties such as
fractions of open base pairs and specific heat.Comment: The Journal of Chemical Physics (2011) in pres
Phonons in aluminum at high temperatures studied by inelastic neutron scattering
Inelastic neutron scattering measurements on aluminum metal were performed at temperatures of 10, 150, 300, 525, and 775 K using direct-geometry Fermi chopper spectrometers. The temperature dependent phonon density of states (DOS) was determined from the scattering, and was used to fit Born–von Kármán models of lattice dynamics. The shifts in the phonon frequencies with increasing temperature were largely explained by the softening of the longitudinal force constants out to third nearest neighbors. A significant broadening of the phonon spectra at high temperatures was also measured. The phonon DOS was used to determine the vibrational contributions to the entropy of aluminum as a function of temperature. All other contributions to the entropy of aluminum were calculated or assessed, and the total entropy was in excellent agreement with the NIST-JANAF compilation [M. W. Chase, J. Phys. Chem. Ref. Data Monogr. 9, 59 (1998)]. Anharmonic effects were attributed to phonon-phonon interactions. The quasiharmonic approximation was generally successful, but its weaknesses are discussed
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