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. $\sim 100$ 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 $\sim 10^7 - 10^8$ 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