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

Charge transport properties of ideal and natural DNA segments, as mutation detectors

DNA sequences of ideal and natural geometries are examined, studying their charge transport properties as mutation detectors. Ideal means textbook geometry. Natural means naturally distorted sequences; geometry taken from available databases. A tight-binding (TB) wire model at the base-pair level is recruited, together with a transfer matrix technique. The relevant TB parameters are obtained using a linear combination of all valence orbitals of all atoms, using geometry, either ideal or natural, as the only input. The investigated DNA sequences contain: (i) point substitution mutations - specifically, the transitions guanine (G) ↔ adenine (A) - and (ii) sequences extracted from human chromosomes, modified by expanding the cytosine-adenine-guanine triplet [(CAG)_n repeats] to mimic the following diseases: (a) Huntington's disease, (b) Kennedy's disease, (c) Spinocerebellar ataxia 6, (d) Spinocerebellar ataxia 7. Quantities such as eigenspectra, density of states, transmission coefficients, and the - more experimentally relevant - current-voltage (I-V) curves are studied, intending to find adequate features to recognize mutations. To this end, the normalised deviation of the I-V curve from the origin (NDIV) is also defined. The features of the NDIV seem to provide a clearer picture, being sensitive to the number of point mutations and allowing to characterise the degree of danger of developing the aforementioned diseases.

Spin-dependent transport in a driven non-collinear antiferromagnetic fractal network

Non-collinear magnetic texture breaks the spin-sublattice symmetry which gives rise to a spin-splitting effect. Inspired by this, we study the spin-dependent transport properties in a non-collinear antiferromagnetic fractal structure, namely, the Sierpinski Gasket (SPG) triangle. We find that though the spin-up and spin-down currents are different, the degree of spin polarization is too weak. Finally, we come up with a proposal, where the degree of spin polarization can be enhanced significantly in the presence of a time-periodic driving field. Such a prescription of getting spin-filtering effect from an unpolarized source in a fractal network is completely new to the best of our knowledge. Starting from a higher generation of SPG to smaller ones, the precise dependencies of driving field parameters, spin-dependent scattering strength, interface sensitivity on spin polarization are critically investigated. The spatial distribution of spin-resolved bond current density is also explored. Interestingly, our proposed setup exhibits finite spin polarization for different spin-quantization axes. Arbitrarily polarized light is considered and its effect is incorporated through Floquet-Bloch ansatz. All the spin-resolved transport quantities are computed using Green's function formalism following the Landauer-Büttiker prescription. In light of the experimental feasibility of such fractal structures and manipulation of magnetic textures, the present work brings forth new insights into spintronic properties of non-collinear antiferromagnetic SPG. This should also entice the AFM spintronic community to explore other fractal structures with the possibility of unconventional features.

LCAO Electronic Structure of Nucleic Acid Bases and Other Heterocycles and Transfer Integrals in B-DNA, Including Structural Variability

To describe the molecular electronic structure of nucleic acid bases and other heterocycles, we employ the Linear Combination of Atomic Orbitals (LCAO) method, considering the molecular wave function as a linear combination of all valence orbitals, i.e., 2s, 2px, 2py, 2pz orbitals for C, N, and O atoms and 1s orbital for H atoms. Regarding the diagonal matrix elements (also known as on-site energies), we introduce a novel parameterization. For the non-diagonal matrix elements referring to neighboring atoms, we employ the Slater–Koster two-center interaction transfer integrals. We use Harrison-type expressions with factors slightly modified relative to the original. We compare our LCAO predictions for the ionization and excitation energies of heterocycles with those obtained from Ionization Potential Equation of Motion Coupled Cluster with Singles and Doubles (IP-EOMCCSD)/aug-cc-pVDZ level of theory and Completely Normalized Equation of Motion Coupled Cluster with Singles, Doubles, and non-iterative Triples (CR-EOMCCSD(T))/aug-cc-pVDZ level of theory, respectively, (vertical values), as well as with available experimental data. Similarly, we calculate the transfer integrals between subsequent base pairs, to be used for a Tight-Binding (TB) wire model description of charge transfer and transport along ideal or deformed B-DNA. Taking into account all valence orbitals, we are in the position to treat deflection from the planar geometry, e.g., DNA structural variability, a task impossible for the plane Hückel approach (i.e., using only 2pz orbitals). We show the effects of structural deformations utilizing a 20mer evolved by Molecular Dynamics.

Effects of Structural Dynamics on Charge Carrier Transfer in B-DNA: A Combined MD and RT-TDDFT Study

Hole transfer along the axis of duplex DNA has been the focus of physical chemistry research for decades, with implications in diverse fields, from nanotechnology to cell oxidative damage. Computational approaches are particularly amenable for this problem, to complement experimental data for interpretation of transfer mechanisms. To be predictive, computational results need to account for the inherent mobility of biological molecules during the time frame of experimental measurements. Here, we address the structural variability of B-DNA and its effects on hole transfer in a combined molecular dynamics (MD) and real-time time-dependent density functional theory (RT-TDDFT) study. Our results show that quantities that characterize the charge transfer process, such as the time-dependent dipole moment and hole population at a specific site, are sensitive to structural changes that occur on the nanosecond time scale. We extend the range of physical properties for which such a correlation has been observed, further establishing the fact that quantitative computational data on charge transfer properties should include statistical averages. Furthermore, we use the RT-TDDFT results to assess an efficient tight-binding method suitable for high-throughput predictions. We demonstrate that charge transfer, although affected by structural variability, on average, remains strong in AA and GG dimers.

Synchronized Oscillations in Double-Helix B-DNA Molecules with Mirror-Symmetric Codons

A fully analytical treatment of the base-pair and codon dynamics in double-stranded DNA molecules is introduced, by means of a realistic treatment that considers different mass values for G, A, T, and C nucleotides and takes into account the intrinsic three-dimensional, helicoidal geometry of DNA in terms of a Hamitonian in cylindrical coordinates. Within the framework of the Peyrard–Dauxois–Bishop model, we consider the coupling between stretching and stacking radial oscillations as well as the twisting motion of each base pair around the helix axis. By comparing the linearized dynamical equations for the angular and radial variables corresponding to the bp local scale with those of the longer triplet codon scale, we report an underlying hierarchical symmetry. The existence of synchronized collective oscillations of the base-pairs and their related codon triplet units are disclosed from the study of their coupled dynamical equations. The possible biological role of these correlated, long-range oscillation effects in double standed DNA molecules containing mirror-symmetric codons of the form XXX, XX’X, X’XX’, YXY, and XYX is discussed in terms of the dynamical equations solutions and their related dispersion relations.

Predicting the DNA Conductance Using a Deep Feedforward Neural Network Model

Double-stranded DNA (dsDNA) has been established as an efficient medium for charge migration, bringing it to the forefront of the field of molecular electronics and biological research. The charge migration rate is controlled by the electronic couplings between the two nucleobases of DNA/RNA. These electronic couplings strongly depend on the intermolecular geometry and orientation. Estimating these electronic couplings for all the possible relative geometries of molecules using the computationally demanding first-principles calculations requires a lot of time and computational resources. In this article, we present a machine learning (ML)-based model to calculate the electronic coupling between any two bases of dsDNA/dsRNA and bypass the computationally expensive first-principles calculations. Using the Coulomb matrix representation which encodes the atomic identities and coordinates of the DNA base pairs to prepare the input dataset, we train a feedforward neural network model. Our neural network (NN) model can predict the electronic couplings between dsDNA base pairs with any structural orientation with a mean absolute error (MAE) of less than 0.014 eV. We further use the NN-predicted electronic coupling values to compute the dsDNA/dsRNA conductance.

Base-Pairs' Correlated Oscillation Effects on the Charge Transfer in Double-Helix B-DNA Molecules

By introducing a suitable renormalization process, the charge carrier and phonon dynamics of a double-stranded helical DNA molecule are expressed in terms of an effective Hamiltonian describing a linear chain, where the renormalized transfer integrals explicitly depend on the relative orientations of the Watson-Crick base pairs, and the renormalized on-site energies are related to the electronic parameters of consecutive base pairs along the helix axis, as well as to the low-frequency phonons' dispersion relation. The existence of synchronized collective oscillations enhancing the π-π orbital overlapping among different base pairs is disclosed from the study of the obtained analytical dynamical equations. The role of these phonon-correlated, long-range oscillation effects on the charge transfer properties of double-stranded DNA homopolymers is discussed in terms of the resulting band structure.

Scaling Law, Confined and Surface Modes in Photonic Fibonacci Stub Structures: Theory and Experiment

We investigate both theoretically and experimentally the properties of electromagnetic waves propagation and localization in periodic and quasi-periodic stub structures of Fibonacci type. Each block constituting the Fibonacci sequence (FS) is composed of an horizontal segment and a vertical stub. The origin of the primary and secondary gaps shown in such systems is discussed. The behaviors and scattering properties of the electromagnetic modes are studied in two geometries, when the FS is inserted horizontally between two semi-infinite waveguides or grafted vertically along a guide. Typical properties of the Fibonacci systems such as the fragmentation of the frequency spectrum, the self-similarity following a scaling law are analyzed and discussed. It is found that certain modes inside these two geometries decrease according to a power law rather than an exponential law and the localization of these modes displays the property of self-similarity around the central gap frequency of the periodic structure where the quasi-periodicity is most effective. Also, the eigenmodes of the FS of different generation order are studied depending on the boundary conditions imposed on its extremities. It is shown that both geometries provide complementary information on the localization of the different modes inside the FS. In particular, in addition to bulk modes, some localized modes induced by both extremities of the system exhibit different behaviors depending on which surface they are localized. The theory is carried out using the Green’s function approach through an analysis of the dispersion relation, transmission coefficient and electric field distribution through such finite structures. The theoretical findings are in good agreement with the experimental results performed by measuring in the radio-frequency range the transmission along a waveguide in which the FS is inserted horizontally or grafted vertically.

Topological spintronics in a polyacetylene molecule device

Using the Su-Schrieffer-Heeger Hamiltonian and exploiting the Green's function method in the framework of the Landauer-Büttiker formalism, the topological and spin dependent electron transport properties of a trans polyacetylene molecule are studied. It is found that molecules with the intracell single carbon-carbon bonding and the even number of monomers in their chains have two edge states and possess topological properties though their Hamiltonians do not respect the chiral symmetry. A perpendicular exchange magnetic field and two perpendicular and transverse electric fields are used to induce and manipulate the quantum spin dependent electron transport properties. The exchange field induces the spin polarization in different electron energy regions which are expanded by stronger exchange fields. Therefore this proposed device works as a perfect spin filter. The spin polarization can be manipulated by applying the perpendicular electric field and remains robust against the transverse electric field variations.

Charge and heat current rectification by a double-dot system within the Coulomb blockade regime

Nanoscale rectifiers are known to have significant nanoelectronic and nanoheatronic applications. In the present work we theoretically analyze rectifying properties of a junction including a couple of quantum dots asymmetrically coupled to the electrodes. The charge and heat current rectification in the system is controlled by the dots occupation numbers and interdot Coulomb interactions. We examine the dependencies of the rectification ratio on the electron energy levels on the dots, on the intensity of electron-electron interactions, on the gate and bias voltages and on the thermal gradients applied across the system. It is shown that the considered double-dot system possesses significant potentialities as a common as well as a heat diode.

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

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.

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

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.