We investigate the distribution of bubble lifetimes and bubble lengths in DNA at physiological temperature, by performing extensive molecular dynamics simulations with the Peyrard-Bishop-Dauxois (PBD) model, as well as an extended version (ePBD) havi
ng a sequence-dependent stacking interaction, emphasizing the effect of the sequences guanine-cytosine (GC)/adenine-thymine (AT) content on these distributions. For both models we find that base pair-dependent (GC vs AT) thresholds for considering complementary nucleotides to be separated are able to reproduce the observed dependence of the melting temperature on the GC content of the DNA sequence. Using these thresholds for base pair openings, we obtain bubble lifetime distributions for bubbles of lengths up to ten base pairs as the GC content of the sequences is varied, which are accurately fitted with stretched exponential functions. We find that for both models the average bubble lifetime decreases with increasing either the bubble length or the GC content. In addition, the obtained bubble length distributions are also fitted by appropriate stretched exponential functions and our results show that short bubbles have similar likelihoods for any GC content, but longer ones are substantially more likely to occur in AT-rich sequences. We also show that the ePBD model permits more, longer-lived, bubbles than the PBD system.
We study the chaotic dynamics of graphene structures, considering both a periodic, defect free, graphene sheet and graphene nanoribbons (GNRs) of various widths. By numerically calculating the maximum Lyapunov exponent, we quantify the chaoticity for
a spectrum of energies in both systems. We find that for all cases, the chaotic strength increases with the energy density, and that the onset of chaos in graphene is slow, becoming evident after more than $10^4$ natural oscillations of the system. For the GNRs, we also investigate the impact of the width and chirality (armchair or zigzag edges) on their chaotic behavior. Our results suggest that due to the free edges the chaoticity of GNRs is stronger than the periodic graphene sheet, and decreases by increasing width, tending asymptotically to the bulk value. In addition, the chaotic strength of armchair GNRs is higher than a zigzag ribbon of the same width. Further, we show that the composition of ${}^{12}C$ and ${}^{13}C$ carbon isotopes in graphene has a minor impact on its chaotic strength.
We discuss the effect of heterogeneity on the chaotic properties of the Peyrard-Bishop-Dauxois nonlinear model of DNA. Results are presented for the maximum Lyapunov exponent and the deviation vector distribution. Different compositions of adenine-th
ymine (AT) and guanine-cytosine (GC) base pairs are examined for various energies up to the melting point of the corresponding sequence. We also consider the effect of the alternation index, which measures the heterogeneity of the DNA chain through the number of alternations between different types (AT or GC) of base pairs, on the chaotic behavior of the system. Biological gene promoter sequences have been also investigated, showing no distinct behavior of the maximum Lyapunov exponent.
In modeling DNA chains, the number of alternations between Adenine-Thymine (AT) and Guanine-Cytosine (GC) base pairs can be considered as a measure of the heterogeneity of the chain, which in turn could affect its dynamics. A probability distribution
function of the number of these alternations is derived for circular or periodic DNA. Since there are several symmetries to account for in the periodic chain, necklace counting methods are used. In particular, Polyas Enumeration Theorem is extended for the case of a group action that preserves partitioned necklaces. This, along with the treatment of generating functions as formal power series, allows for the direct calculation of the number of possible necklaces with a given number of AT base pairs, GC base pairs and alternations. The theoretically obtained probability distribution functions of the number of alternations are accurately reproduced by Monte Carlo simulations and fitted by Gaussians. The effect of the number of base pairs on the characteristics of these distributions is also discussed, as well as the effect of the ratios of the numbers of AT and GC base pairs.
We introduce a torsional force field for sp$^2$ carbon to augment an in-plane atomistic potential of a previous work (Kalosakas et al, J. Appl. Phys. {bf 113}, 134307 (2013)) so that it is applicable to out-of-plane deformations of graphene and relat
ed carbon materials. The introduced force field is fit to reproduce DFT calculation data of appropriately chosen structures. The aim is to create a force field that is as simple as possible so it can be efficient for large scale atomistic simulations of various sp$^2$ carbon structures without significant loss of accuracy. We show that the complete proposed potential reproduces characteristic properties of fullerenes and carbon nanotubes. In addition, it reproduces very accurately the out-of-plane ZA and ZO modes of graphenes phonon dispersion as well as all phonons with frequencies up to 1000~cm$^{-1}$.
We present a simple torsional potential for graphene to accurately describe its out-of-plane deformations. The parameters of the potential are derived through appropriate fitting with suitable DFT calculations regarding the deformation energy of grap
hene sheets folded around two different folding axes, along an armchair or along a zig-zag direction. Removing the energetic contribution of bending angles, using a previously introduced angle bending potential, we isolate the purely torsional deformation energy, which is then fitted to simple torsional force fields. The presented out-of-plane torsional potential can accurately fit the deformation energy for relatively large torsional angles up to 0.5 rad. To test our proposed potential, we apply it to the problem of the vertical displacement of a single carbon atom out of the graphene plane and compare the obtained deformation energy with corresponding DFT calculations. The dependence of the deformation energy on the vertical displacement of the pulled carbon atom is indistinguishable in these two cases, for displacements up to about 0.5 $AA$. The presented potential is applicable to other sp$^2$ carbon structures.
