Electronic structure and carrier transfer in B-DNA monomer polymers and dimer polymers: Stationary and time-dependent aspects of wire model vs. extended ladder model

We employ two Tight-Binding (TB) approaches to study the electronic structure and hole or electron transfer in B-DNA monomer polymers and dimer polymers made up of $N$ monomers (base pairs): (I) at the base-pair level, using the on-site energies of base pairs and the hopping integrals between successive base pairs, i.e., a wire model and (II) at the single-base level, using the on-site energies of the bases and the hopping integrals between neighboring bases, i.e., an \textit{extended} ladder model since we also include diagonal hoppings. We solve a system of $MD$ ("matrix dimension") coupled equations [(I) $MD$ = $N$, (II) $MD$ = $2N$] for the time-independent problem, and a system of $MD$ coupled $1^\text{st}$ order differential equations for the time-dependent problem. We study the HOMO and the LUMO eigenspectra, the occupation probabilities, the Density of States (DOS) and the HOMO-LUMO gap as well as the mean over time probabilities to find the carrier at each site [(I) base pair or (II) base)], the Fourier spectra, which reflect the frequency content of charge transfer (CT) and the pure mean transfer rates from a certain site to another. The two TB approaches give coherent, complementary aspects of electronic properties and charge transfer in B-DNA monomer polymers and dimer polymers.Comment: 20 pages, 23 figure

Quasi-periodic and fractal polymers: Energy structure and carrier transfer

We study the energy structure and the coherent transfer of an extra electron or hole along aperiodic polymers made of $N$ monomers, with fixed boundaries, using B-DNA as our prototype system. We use a Tight-Binding wire model, where a site is a monomer (e.g., in DNA, a base pair). We consider quasi-periodic (Fibonacci, Thue-Morse, Double-Period, Rudin-Shapiro) and fractal (Cantor Set, Asymmetric Cantor Set) polymers made of the same monomer (I polymers) or made of different monomers (D polymers). For all types of such polymers, we calculate the HOMO and LUMO eigenspectrum, the HOMO-LUMO gap and the density of states. We examine the mean over time probability to find the carrier at each monomer, the frequency content of carrier transfer (Fourier spectra, weighted mean frequency of each monomer, total weighted mean frequency of the polymer), and the pure mean transfer rate $k$. Our results reveal that there is a correspondence between the degree of structural complexity and the transfer properties. I polymers are more favorable for charge transfer than D polymers. We compare $k(N)$ of quasi-periodic and fractal sequences with that of periodic sequences (including homopolymers) as well as with randomly shuffled sequences. Finally, we discuss aspects of experimental results on charge transfer rates in DNA with respect to our coherent pure mean transfer rates.Comment: 19 pages, 13 figures. arXiv admin note: text overlap with arXiv:1808.0561

Symmetry and Asymmetry in Quasicrystals or Amorphous Materials

About forty years after its discovery, it is still common to read in the literature that quasicrystals (QCs) occupy an intermediate position between amorphous materials and periodic crystals. However, QCs exhibit high-quality diffraction patterns containing a collection of discrete Bragg reflections at variance with amorphous phases. Accordingly, these materials must be properly regarded as long-range ordered materials with a symmetry incompatible with translation invariance. This misleading conceptual status can probably arise from the use of notions borrowed from the amorphous solids framework (such us tunneling states, weak interference effects, variable range hopping, or spin glass) in order to explain certain physical properties observed in QCs. On the other hand, the absence of a general, full-fledged theory of quasiperiodic systems certainly makes it difficult to clearly distinguish the features related to short-range order atomic arrangements from those stemming from long-range order correlations. The contributions collected in this book aim at gaining a deeper understanding on the relationship between the underlying structural order and the resulting physical properties in several illustrative aperiodic systems, including the border line between QCs and related complex metallic alloys, hierarchical superlattices, electrical transmission lines, nucleic acid sequences, photonic quasicrystals, and optical devices based on aperiodic order designs

Charge transport in cancer-related genes and early carcinogenesis

The electronic transmission properties of DNA molecules are believed to play a significant role in many physical phenomena taking place in living organisms (Chakraborty 2007) [1] Here we study the charge transport (CT) properties of cancer-related genes including some of the most important tumor suppressors We find that the changes in averaged CT around the sites of pathogenic and cancerous mutations are statistically smaller than those on sites where pathogenic mutations have not been observed The results suggest that CT might be an indicator to discriminate between pathogenic and non-pathogenic mutations at an early stage Mutations which cause little change in CT may be more likely to occur or more likely to be missed by damage-repair enzymes which probe CT and are therefore more likely to persist and cause disease Crown Copyright (C) 2010 Published by Elsevier BV All rights reserve