G. Kalosakas

Sequence-specific thermal fluctuations identify start sites for DNA transcription

We report successful comparisons between model predictions for intrinsic thermal openings and experimental transcription data, showing that large and slow thermally induced openings (bubbles) of double-stranded DNA coincide with the location of start sites for transcription. Investigating viral and bacteriophage DNA gene promoter segments, we find that the largest opening occurs at the transcription start site in all cases studied. Other probable large openings predicted in our model appear to be related to other regulatory sites. The coherent dynamics is determined by a combination of sequence specificity (disorder), nonlinearity, and entropy, controlled by the long-range consequences of local base-pair stacking constraints.

Charge trapping in DNA due to intrinsic vibrational hot spots

We study temperature effects on the characteristic time for which charge carriers remain spatially confined while interacting with fluctuational openings (bubbles) of double stranded DNA. Using semiclassical molecular-dynamics simulations, we find that in the low-temperature regime this characteristic time decreases in a power-law fashion with temperature and coincides with the polaronic lifetime. However, above 50–70 K the confinement time exhibits an exponential increase with temperature. We demonstrate that this enhanced trapping is a result of intrinsic dynamical structural disorder resulting from thermal fluctuations. Specifically, nonlinearity-induced hot spots in the lattice subsystem form breathing potential barriers confining the charge for substantially longer times.

Phonon properties of graphene derived from molecular dynamics simulations

A method that utilises atomic trajectories and velocities from molecular dynamics simulations has been suitably adapted and employed for the implicit calculation of the phonon dispersion curves of graphene. Classical potentials widely used in the literature were employed. Their performance was assessed for each individual phonon branch and the overall phonon dispersion, using available inelastic x-ray scattering data. The method is promising for systems with large scale periodicity, accounts for anharmonic effects and non-bonding interactions with a general environment, and it is applicable under finite temperatures. The temperature dependence of the phonon dispersion curves has been examined with emphasis on the doubly degenerate Raman active Γ-E2g phonon at the zone centre, where experimental results are available. The potentials used show diverse behaviour. The Tersoff-2010 potential exhibits the most systematic and physically sound behaviour in this regard, and gives a first-order temperature coefficient of χ = −0.05 cm−1/K for the Γ-E2g shift in agreement with reported experimental values.

Electronic parameters for charge transfer along DNA

Abstract.We systematically examine all the tight-binding parameters pertinent to charge transfer along DNA. The

Dependence on temperature and guanine-cytosine content of bubble length distributions in DNA

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Graphene flakes under controlled biaxial deformation

molecular structure of the four DNA bases (adenine, thymine, cytosine, and guanine) is investigated by using the linear combination of atomic orbitals method with a recently introduced parametrization. The HOMO and LUMO wave functions and energies of DNA bases are discussed and then used for calculating the corresponding wave functions of the two B-DNA base-pairs (adenine-thymine and guanine-cytosine). The obtained HOMO and LUMO energies of the bases are in good agreement with available experimental values. Our results are then used for estimating the complete set of charge transfer parameters between neighboring bases and also between successive base-pairs, considering all possible combinations between them, for both electrons and holes. The calculated microscopic quantities can be used in mesoscopic theoretical models of electron or hole transfer along the DNA double helix, as they provide the necessary parameters for a tight-binding phenomenological description based on the

Distribution of bubble lengths in DNA.

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Analytical and numerical study of diffusion-controlled drug release from composite spherical matrices.

molecular overlap. We find that usually the hopping parameters for holes are higher in magnitude compared to the ones for electrons. Our findings are also compared with existing calculations from first principles.

Nonlocal interactions in doped cuprates : Correlated motion of Zhang-Rice polarons

We present numerical results on the temperature dependence of the distribution of bubble lengths in DNA segments of various guanine-cytosine (GC) concentrations. Base-pair openings are described by the Peyrard-Bishop-Dauxois model and the corresponding thermal equilibrium distributions of bubbles are obtained through Monte Carlo calculations for bubble sizes up to the order of a hundred base pairs. The dependence of the parameters of bubble length distribution on temperature and the GC content is investigated. We provide simple expressions which approximately describe these relations. The variation of the average bubble length is also presented. We find a temperature dependence of the exponent c that appears in the distribution of bubble lengths. If an analogous dependence exists in the loop entropy exponent of real DNA, it may be relevant to understand overstretching in force-extension experiments.

POSSIBILITY OF OBSERVATION OF POLARON NORMAL MODES AT THE FAR-INFRARED SPECTRUM OF ACETANILIDE AND RELATED ORGANICS

Thin membranes, such as monolayer graphene of monoatomic thickness, are bound to exhibit lateral buckling under uniaxial tensile loading that impairs its mechanical behaviour. In this work, we have developed an experimental device to subject 2D materials to controlled equibiaxial strain on supported beams that can be flexed up or down to subject the material to either compression or tension, respectively. Using strain gauges in tandem with Raman spectroscopy measurements, we monitor the G and 2D phonon properties of graphene under biaxial strain and thus extract important information about the uptake of stress under these conditions. The experimental shift over strain for the G and 2D Raman peaks were found to be in the range of 62.3 ± 5 cm–1/%, and 148.2 ± 6 cm–1/%, respectively, for monolayer but also bilayer graphenes. The corresponding Grüneisen parameters for the G and 2D peaks were found to be between 1.97 ± 0.15 and 2.86 ± 0.12, respectively. These values agree reasonably well with those obtained from small-strain bubble-type experiments. The results presented are also backed up by classical and ab initio molecular dynamics simulations and excellent agreement of Γ-E2g shifts with strains and the Grüneisen parameter was observed.