Wire and extended ladder model predict THz oscillations in DNA monomers, dimers and trimers

Abstract

Abstract. We call monomer a B-DNA base pair and study, analytically and numerically, electron or hole oscillations in monomers, dimers and trimers. We employ two Tight Binding (TB) approaches: (I) at the base-pair level, using the on-site energies of the base pairs and the hopping parameters 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 parameters between neighbouring bases, specifically between (a) two successive bases in the same strand, (b) complementary bases that define a base pair, and (c) diagonally located bases of successive base pairs, i.e. an extended ladder model since it also includes the diagonal hoppings (c). For monomers, with TB II, we predict periodic carrier oscillations with frequency f ≈ 50-550 THz. For dimers, with TB I, we predict periodic carrier oscillations with f ≈ 0.25-100 THz. For trimers made of identical monomers, with TB I, we predict periodic carrier oscillations with f ≈ 0.5-33 THz. In other cases, either with TB I or TB II, the oscillations may be not strictly periodic, but Fourier analysis shows similar frequency content. For dimers and trimers, TB I and TB II are successfully compared giving complementary aspects of the oscillations.

RT-TDDFT study of hole oscillations in B-DNA monomers and dimers

“…We observe that for dimers made of identical monomers, where p ≈ 1, we have P i ≈ P f ≈ 0.5, while for dimers made of different monomers P i ≈ 1 and P f ≈ 0, with the exception of the GA dimer. This, again, agrees qualitatively with the TB picture [8,17,18].…”

“…Our calculations for the cases AT(01), TA(01), GC(01), and CG(01) are not included in Fig.1, since they are identical with the cases AT(10), TA(10), GC(10), CG(10), respectively, as expected from base-pair symmetry and found also in Refs. [8,17,18].…”

Spectral and transmission properties of periodic 1D tight-binding lattices with a generic unit cell: an analysis within the transfer matrix approach

“…Equation (15) and the formula connecting the Chebyshev polynomials of the first and second kind, [47], lead to an alternate form from which the eigenvalues for cyclic boundaries can be found, i.e.…”

“…are polynomial equations of E of the same degree (N) that are mutually satisfied [35], equation (17) produces the eigenvalues of the tridiagonal symmetric u-Toeplitz matrix of size mu. Exploiting equations (14)- (15), the determination of these eigenvalues is reduced to the solution of…”

Periodic, quasiperiodic, fractal, Kolakoski, and random binary polymers: Energy structure and carrier transport

“…The on-site energies are taken E A−T = −8.3 eV for the A-T base pair and E G−C = −8.0 eV for the G-C base pair. 5,6,17,36,49 The hopping integrals between successive base pairs that are involved in the segments studied here are shown in Table I. 5,6,17,36,49 The values of the parameters correspond to the HOMO of the base pairs and are discussed in Ref.…”