DNA-based nanobiostructured devices: The role of quasiperiodicity and correlation effects

Albuquerque, E.L.; Fulco, U. L.; Freire, V. N.; Caetano, E. W. S.; Lyra, M. L.; Moura, F. A. B. F. de

doi:10.1016/j.physrep.2013.10.004

Cited by 100 publications

(55 citation statements)

References 296 publications

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“…The former can provide a more detailed description, but are currently limited to very short segments, while the latter are much less detailed but allowing to address systems of realistic length, grasping hopefully the underlying physics 39 . Here we study rather long B-DNA segments, hence we adopt the latter approach.…”

Section: Introductionmentioning

confidence: 99%

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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

et al. 2016

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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 extended ladder model since we also include diagonal hoppings. We solve a system of M D ("matrix dimension") coupled equations [(I) M D = N , (II) M D = 2N ] for the time-independent problem, and a system of M D coupled 1 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.

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Section: Introductionmentioning

confidence: 99%

“…We need the onsite energies of bases and the hopping integrals between neighboring bases. We also include diagonal hoppings, in that sense, TB II is an extended ladder model 39 . The inclusion of diagonal hoppings is crucial in some cases as will become evident below.…”

Section: Introductionmentioning

confidence: 99%

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

et al. 2016

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“…Intra-strand Stacking Forces A major computational task arises when stacking forces are introduced to pile up the nucleotides along the strands. While long range correlations should be taken into account in models for DNA coherent charge transport [23], the thermodynamic quantities are generally dominated by short range correlations [24,25]. This brings about a two particles potential that couples fluctuational paths between adjacent bases whose flat surfaces are perpendicular to the helix axis.…”

Section: B Inter-strand Forcesmentioning

confidence: 99%

Entropic penalties in circular DNA assembly

Zoli

2014

The Journal of Chemical Physics

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The thermodynamic properties of DNA circular molecules are investigated by a new path integral computational method which treats in the real space the fundamental forces stabilizing the molecule. The base pair and stacking contributions to the classical action are evaluated separately by simulating a broad ensemble of twisted conformations. We obtain, for two short sequences, a free energy landscape with multiple wells corresponding to the most convenient values of helical repeat. Our results point to a intrinsic flexibility of the circular structures in which the base pair fluctuations move the system from one well to the next thus causing the local unwinding of the helix. The latter is more pronounced in the shorter sequence whose cyclization causes a higher bending stress. The entropic reductions associated to the formation of the ordered helicoidal structure are estimated.

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“…Many researchers, especially ones in theoretical physics and nonlinear dynamics and also triggered the formulation of several simple models of nonlinear DNA dynamics corresponding to geometric structure, namely, the DNA double-stranded [3][4][5][6][7][8][9][10][11][12][13][14] or the double helix [15][16][17][18][19][20][21][22][23][24][25][26][27][28]. These models had been developed during the past decade to describe the nonlinear dynamics properties of open base-pairs in DNA, which commonly called denaturation bubbles [29]. In 1964 Robin Holliday has a well-proposed that double structures of DNA a four-stranded junction would be involved as an intermediate to allow reciprocal exchange of genetic information through recombination across two homologous DNA duplexes [30,31].…”

Section: Introductionmentioning

confidence: 99%

On The Features Solitary Wave Solutions for the DoubleStructures Model of DNA

2017

International Journal of Research Studies in Biosciences

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DNA-based nanobiostructured devices: The role of quasiperiodicity and correlation effects

Cited by 100 publications

References 296 publications

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

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

Entropic penalties in circular DNA assembly

On The Features Solitary Wave Solutions for the DoubleStructures Model of DNA

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