title: Electronic structure and carrier transfer in B-DNA monomer polymers and dimer polymers: Stationary and time-dependent aspects of a wire model versus an extended ladder model.
abstract: We employ two tight-binding (TB) approaches to systematically 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 onsite 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 onsite energies of the bases and the hopping integrals between neighboring bases, i.e., an extended ladder model since we also include diagonal hoppings. We solve a system of M (matrix dimension) coupled equations [(I) M=N, (II) M=2N] for the time-independent problem, and a system of M coupled first order differential equations for the time-dependent problem. We perform a comparative study of stationary and time-dependent aspects of the two TB variants, using realistic sets of parameters. The studied properties include HOMO and LUMO eigenspectra, occupation probabilities, density of states and HOMO-LUMO gaps as well as mean over time probabilities to find the carrier at each site [(I) base pair or (II) base], Fourier spectra, which reflect the frequency content of charge transfer, and 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.
authors.affiliation: National and Kapodistrian University of Athens, Department of Physics, Panepistimiopolis, 15784 Zografos, Athens, Greece.
authors.forename: K
authors.initials: K
authors.lastname: Lambropoulos
authors.affiliation: National and Kapodistrian University of Athens, Department of Physics, Panepistimiopolis, 15784 Zografos, Athens, Greece.
authors.forename: M
authors.initials: M
authors.lastname: Chatzieleftheriou
authors.affiliation: National and Kapodistrian University of Athens, Department of Physics, Panepistimiopolis, 15784 Zografos, Athens, Greece.
authors.forename: A
authors.initials: A
authors.lastname: Morphis
authors.affiliation: National and Kapodistrian University of Athens, Department of Physics, Panepistimiopolis, 15784 Zografos, Athens, Greece.
authors.forename: K
authors.initials: K
authors.lastname: Kaklamanis
authors.affiliation: National and Kapodistrian University of Athens, Department of Physics, Panepistimiopolis, 15784 Zografos, Athens, Greece.
authors.forename: R
authors.initials: R
authors.lastname: Lopp
authors.affiliation: National and Kapodistrian University of Athens, Department of Physics, Panepistimiopolis, 15784 Zografos, Athens, Greece.
authors.forename: M
authors.initials: M
authors.lastname: Theodorakou
authors.affiliation: National and Kapodistrian University of Athens, Department of Physics, Panepistimiopolis, 15784 Zografos, Athens, Greece.
authors.forename: M
authors.initials: M
authors.lastname: Tassi
authors.affiliation: National and Kapodistrian University of Athens, Department of Physics, Panepistimiopolis, 15784 Zografos, Athens, Greece.
authors.forename: C
authors.initials: C
authors.lastname: Simserides
mesh_terms: D020029:Base Pairing; D059371:DNA, B-Form / Q000737:chemistry*; D055724:Electrophysiological Phenomena; D008954:Models, Biological; D011108:Polymers / Q000737:chemistry*; D013057:Spectrum Analysis
chemical_list: D059371:DNA, B-Form; D011108:Polymers