Periodic polymers with increasing repetition unit: Energy structure and carrier transfer

Lambropoulos, Konstantinos; Vantaraki, Christina; Bilia, P.; Mantela, Marilena; Simserides, Constantinos

doi:10.1103/physreve.98.032412

Cited by 12 publications

(30 citation statements)

References 69 publications

(89 reference statements)

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“…Several techniques can be applied to solve the models, depending on what is studied, such as the numerical diagonalization of the Hamiltonian in Equation 2 [47,56,57], the transfer matrix method [58][59][60] outlined above, and the Non-Equilibrium Green's Function technique [61]. As it is apparent from Equation 3, the transfer matrix method is not applicable if the matrices τ τ τ n are singular.…”

Section: Additional Remarksmentioning

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: Additional Remarksmentioning

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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“…In TBI,

and

. Details and discussions of various aspects of the TBI wire model can be found elsewhere [ 5 , 33 , 34 , 35 , 36 , 37 ]. In TBImod,

and

.…”

Section: Tight-binding Wire Model Variantsmentioning

confidence: 99%

Hole Transfer in Open Carbynes

2020

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We investigate hole transfer in open carbynes, i.e., carbon atomic nanowires, using Real-Time Time-Dependent Density Functional Theory (RT-TDDFT). The nanowire is made of N carbon atoms. We use the functional B3LYP and the basis sets 3-21G, 6-31G*, cc-pVDZ, cc-pVTZ, cc-pVQZ. We also utilize a few Tight-Binding (TB) wire models, a very simple model with all sites equivalent and transfer integrals given by the Harrison ppπ expression (TBI) as well as a model with modified initial and final sites (TBImod) to take into account the presence of one or two or three hydrogen atoms at the edge sites. To achieve similar site occupations in cumulenes with those obtained by converged RT-TDDFT, TBImod is sufficient. However, to achieve similar frequency content of charge and dipole moment oscillations and similar coherent transfer rates, the TBImod transfer integrals have to be multiplied by a factor of four (TBImodt4times). An explanation for this is given. Full geometry optimization at the B3LYP/6-31G* level of theory shows that in cumulenes bond length alternation (BLA) is not strictly zero and is not constant, although it is symmetrical relative to the molecule center. BLA in cumulenic cases is much smaller than in polyynic cases, so, although not strictly, the separation to cumulenes and polyynes, approximately, holds. Vibrational analysis confirms that for N even all cumulenes with coplanar methylene end groups are stable, for N odd all cumulenes with perpendicular methylene end groups are stable, and the number of hydrogen atoms at the end groups is clearly seen in all cumulenic and polyynic cases. We calculate and discuss the Density Functional Theory (DFT) ground state energy of neutral molecules, the CDFT (Constrained DFT) “ground state energy” of molecules with a hole at one end group, energy spectra, density of states, energy gap, charge and dipole moment oscillations, mean over time probabilities to find the hole at each site, coherent transfer rates, and frequency content, in general. We also compare RT-TDDFT with TB results.

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“…using various natural and artificial nucleobases with different highest occupied molecular orbital (HOMO) levels 4 . Transfer rates can be increased by many orders of magnitude with appropriate sequence choice [5][6][7] . Furthermore, dynamical fluctuations, arising from either solvent fluctuations or base-pair vibrations can gate charge transport, counteracting the intrinsic disordered potential profile of the sequence 8 .…”

Section: Introductionmentioning

confidence: 99%

“…Several works have been devoted to the study of transfer and transport in specific DNA structures (periodic [5][6][7]28,29 , quasiperiodic [30][31][32] , random and natural 19,20,[33][34][35] ) using variants of the Tight-Binding (TB) method. Here, we employ the TB wire model, with the sites of the chain being the base pairs, to study the spectral, localization and charge transport properties of periodic, deterministic aperiodic [Thue-Morse (TM), Fibonacci (F), Period Doubling (PD), Rudin-Shapiro (RS), Cantor set (CS), generalized Cantor set (GCS), Kolakoski (KOL)] and random DNA binary segments.…”

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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Periodic polymers with increasing repetition unit: Energy structure and carrier transfer

Cited by 12 publications

References 69 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

Hole Transfer in Open Carbynes

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

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