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

Tassi, Maria; Morphis, A.; Lambropoulos, Konstantinos; Simserides, Constantinos

doi:10.1080/23311940.2017.1361077

Cited by 17 publications

(22 citation statements)

References 41 publications

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“…There are many external (aqueousness, presence of counterions, extraction process, electrodes, contacts, purity, substrate), and internal (such as the base-pair sequence and geometry) factors that affect carrier motion along nucleic acids. Both ab initio calculations [14][15][16][17][18][19][20][21][22] and model Hamiltonians [23][24][25][26][27][28][29][30][31][32][33][34] have been used to theoretically explore the variety of experimental results that predict electrical behavior ranging from metallic to insulating, as well as the underlying mechanisms.…”

Section: Introductionmentioning

confidence: 99%

Tight-Binding Modeling of Nucleic Acid Sequences: Interplay between Various Types of Order or Disorder and Charge Transport

Lambropoulos

Simserides

2019

Symmetry

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This review is devoted to tight-binding (TB) modeling of nucleic acid sequences like DNA and RNA. It addresses how various types of order (periodic, quasiperiodic, fractal) or disorder (diagonal, non-diagonal, random, methylation et cetera) affect charge transport. We include an introduction to TB and a discussion of its various submodels [wire, ladder, extended ladder, fishbone (wire), fishbone ladder] and of the process of renormalization. We proceed to a discussion of aperiodicity, quasicrystals and the mathematics of aperiodic substitutional sequences: primitive substitutions, Perron–Frobenius eigenvalue, induced substitutions, and Pisot property. We discuss the energy structure of nucleic acid wires, the coupling to the leads, the transmission coefficients and the current–voltage curves. We also summarize efforts aiming to examine the potentiality to utilize the charge transport characteristics of nucleic acids as a tool to probe several diseases or disorders.

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Section: Introductionmentioning

confidence: 99%

Tight-Binding Modeling of Nucleic Acid Sequences: Interplay between Various Types of Order or Disorder and Charge Transport

Lambropoulos

Simserides

2019

Symmetry

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“…This is demonstrated in Fig. 9, where the I-V curve of a periodic (GA) 16 segment is determined as a function of E M . It is evident that larger currents (∼ 0.1 µA) occur at small biases when E M lies within the bands of the segment.…”

Section: Current-voltage Curvesmentioning

confidence: 94%

“…Hence, the need for a better understanding of the intrinsic factors that affect charge transfer and transport, such as geometry and base-pair sequence, arises. Ab initio calculations [10][11][12][13][14][15][16] and model Hamiltonians [5][6][7][17][18][19][20][21][22][23][24][25][26][27] have been used to explore the variety of experimental results and the underlying mechanisms. The former are currently limited to short segments for computational reasons, while the latter allow to address systems of realistic length.…”

Section: Introductionmentioning

confidence: 99%

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

Lambropoulos

Simserides

2019

Phys. Rev. E

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We study periodic, quasi-periodic (Thue-Morse, Fibonacci, Period Doubling, Rudin-Shapiro), fractal (Cantor, generalized Cantor), Kolakoski and random binary sequences using a tight-binding wire model, where a site is a monomer (e.g., in DNA, a base pair). We use B-DNA as our prototype system. All sequences have purines, guanine (G) or adenine (A) on the same strand, i.e., our prototype binary alphabet is (G,A). Our aim is to examine the influence of sequence intricacy and magnitude of parameters on energy structure, localization and charge transport. We study quantities such as autocorrelation function, eigenspectra, density of states, Lyapunov exponents, transmission coefficients and current-voltage curves. We show that the degree of sequence intricacy and the presence of correlations decisively affect the aforementioned physical properties. Periodic segments have enhanced transport properties. Specifically, in homogeneous sequences transport efficiency is maximum. There are several deterministic aperiodic sequences that can support significant currents, depending on the Fermi level of the leads. Random sequences is the less efficient category.

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“…The aim of this work is a comparative examination of the influence of base-pair sequence on charge transfer, in aperiodic sequences. Ab initio calculations [40,41,42,43,44,45,46,47,48], used to explore experimental results and the underlying mechanisms, are currently limited to short segments for computational reasons. Here, we study rather long sequences, so we employ the Tight-Binding (TB) model which allows for addressing systems of realistic length [14,15,16,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65].…”

Section: Introductionmentioning

confidence: 99%

Quasi-Periodic and Fractal Polymers: Energy Structure and Carrier Transfer

et al. 2019

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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 highest occupied molecular orbital (HOMO) eigenspectrum and the lowest unoccupied molecular orbital (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.

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

Cited by 17 publications

References 41 publications

Tight-Binding Modeling of Nucleic Acid Sequences: Interplay between Various Types of Order or Disorder and Charge Transport

Tight-Binding Modeling of Nucleic Acid Sequences: Interplay between Various Types of Order or Disorder and Charge Transport

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

Quasi-Periodic and Fractal Polymers: Energy Structure and Carrier Transfer

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